Resource Type:
Polypeptide
Name:
DCAR_008800
Identifier:
DCAR_008800.mRNA-protein
Sequence:
MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSFFSSASCSVERCSFA
SESSQQHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDT
KVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLN
NTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSS
ERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRP
SFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTP
GVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRS
SDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTS
GVLPIVEWQDSHFPKHVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDW
KKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLE
MKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISF
RRTRQISSLSGCFTCHAL*
Sequence Length:
569
Sequence Checksum:
41800b9972b207b535750d1fd733bdd7
View location in JBrowse:
Organism:
Relationship:
| Relationships |
|---|
| The polypeptide, DCAR_008800, derives from mRNA, DCAR_008800. |
Blast Results:
The following BLAST results are available for this feature:
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B6Z911 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 657.136 bits (1694), Expect = 0.000e+0
Identity = 354/579 (61.14%), Postives = 427/579 (73.75%), Query Frame = 0
Match: A0A5B6Z911 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 657.136 bits (1694), Expect = 0.000e+0
Identity = 354/579 (61.14%), Postives = 427/579 (73.75%), Query Frame = 0
Query: 2 PELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFASESSQ---------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
PELGFQ N +SG ARD SPDSVIF+ ES+F FSSAS SV+RCSFAS+ QH A ++ E+SS GPD PN ST++KNS ++V+K+KV+++D + ET+DENQ LDSARSSFSQALK+CQ RRS+ EALL+K DRR P SLDLNN++ N +SSPR GV+KK+ +TR TGT PSPG PN+ TS +QKGWSSERV L + NRRHV LLP+N+ RTLPSKWEDAERWIFSPV+GD RPSF QP RRPK+KSGPLGPP Y+S++SPAV +F+GG V N M SPF+ GV+AAD LS++ + G F EPC+ RSVS+HGCS L QS L S D + D +D +IS VS+RDMATQMSPE SPHSS K R S + STS LPIVE H K VRDVQVDERVT+++W K K TG+GS + DDWKKKA E +S+ WEVS+TA + S KREEA+I AWENLQKAKAEA IRKLEMKLEKKRSSSM+KIM K ++A++KA++MRSS + S A Q + TSHK+ISFRRTR+ISSLSGCFTCHA
Sbjct: 3 PELGFQDQ-NLLTSGYR-ARDFSPDSVIFTVESNFSLFSSASGSVDRCSFASDVHDHDSLVSEISQHFAGNDLPETSS-GPDPDPNRSTIHKNSCLVKKVEKAKVQKEDNEAETEDENQTLDSARSSFSQALKECQDRRSRSEALLRKPDRRRPASLDLNNSIANAINSSPRFGVMKKNSVLTRRTGTFPSPGTPNYQHTSVGIQKGWSSERVPLHANANRRHVGAALLPFNSGRTLPSKWEDAERWIFSPVAGDGLVRPSFPQPQRRPKSKSGPLGPPGIVYHSLFSPAVPLFEGGNVGNLMAGSPFSTGVMAADGLSIRCGGDHGGGGRFP---EPCMARSVSVHGCSALLSQSSLPGSQDEELDGVKDAATHISRAVSRRDMATQMSPEGSPHSSPKRRPSLSLSTSSALPIVELPSVHSSKLEVRDVQVDERVTVTRWSKKHKARFTGKGSENVDDWKKKAAEARSSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAEIRKLEMKLEKKRSSSMDKIMNKLRSAQRKAQEMRSSVIASQAHQVARTSHKVISFRRTRRISSLSGCFTCHAF 575
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B6Z6L8 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763} (Fragment))
HSP 1 Score: 655.21 bits (1689), Expect = 0.000e+0
Identity = 352/580 (60.69%), Postives = 426/580 (73.45%), Query Frame = 0
Match: A0A5B6Z6L8 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763} (Fragment))
HSP 1 Score: 655.21 bits (1689), Expect = 0.000e+0
Identity = 352/580 (60.69%), Postives = 426/580 (73.45%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFASESSQ---------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
MPELGFQ N +SG ARD SPDSVIF+ ES+F FSSAS SV+RCSFAS+ QH A ++ E+SS GPD PN ST++KNS ++V+K+KV+++D + ET+DENQ LDSARSSFSQALK+CQ RRS+ EALL+K DRR P SLDLNN++ N +SSPR GV+KK+ +TR TGT PSPG PN+ TS +QKGWSSERV L + NRRHV LLP+N+ RTLPSKWEDAERWIFSPV+GD RPSF QP RRPK+KSGPLGPP Y+S++SPAV +F+GG V N M SPF+ GV+AAD LS++ + G F EPC+ RSVS+HGCS L QS L S D + D +D +IS VS+RDMATQMSPE SPHSS K R S + STS LPIVE H K VRDVQVDERVT+++W K K TG+GS + DDWKKKA E +S+ WEVS+TA + S KREEA+I AWENLQKAKAEA IRKLEMKLEKKRSSSM+KI+ K ++A++KA+ MRSS + + A Q + TSHK+ISFRR +QISSLSGCFTCHA
Sbjct: 12 MPELGFQDQ-NLLTSGYR-ARDFSPDSVIFTVESNFSLFSSASGSVDRCSFASDVHDHDSLVSEISQHFAGNDLPETSS-GPDPDPNRSTIHKNSCLVKKVEKAKVQKEDNEAETEDENQTLDSARSSFSQALKECQDRRSRSEALLRKPDRRRPASLDLNNSIANAINSSPRFGVMKKNSVLTRRTGTFPSPGTPNYQHTSVGIQKGWSSERVPLHANANRRHVGAALLPFNSGRTLPSKWEDAERWIFSPVAGDGLVRPSFPQPQRRPKSKSGPLGPPGIVYHSLFSPAVPLFEGGNVGNLMAGSPFSTGVMAADGLSIRCGGDHGGGGRFP---EPCMARSVSVHGCSALLSQSSLPGSQDEELDGVKDAATHISRAVSRRDMATQMSPEGSPHSSPKRRPSLSLSTSSALPIVELPSVHSSKLEVRDVQVDERVTVTRWSKKHKARFTGKGSENVDDWKKKAAEARSSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAEIRKLEMKLEKKRSSSMDKILNKLRSAQRKAQDMRSSVIANQAHQVARTSHKVISFRRAQQISSLSGCFTCHAF 585
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B6Z7B8 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 629.017 bits (1621), Expect = 0.000e+0
Identity = 351/580 (60.52%), Postives = 414/580 (71.38%), Query Frame = 0
Match: A0A5B6Z7B8 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 629.017 bits (1621), Expect = 0.000e+0
Identity = 351/580 (60.52%), Postives = 414/580 (71.38%), Query Frame = 0
Query: 2 PELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFAS----------ESSQQHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
PELGFQ N G RDVSPDSVIF+ ES+F FSSAS SV+RCSFAS E SQ+HLA H+ ESSS GPD PN+STV KNS S+ V+K KV+++D + ET D NQ LDS RSSFSQA+K+CQ RRS++EALL++ DRR P SLDLNN +TN TSSSPR GV+KK+ +GT PSPG PN+ S +QKGWSSERV L + NRRHV LP+NN RTLPSKWEDAERWIFSP++GD +RPSF QP RR K+KSGPLGPP AYYS+YSPAV M +GG V N M SPF+ GV+ AD LS+Q G G F + MEPC+ RSVS+HGCS L QS L S D K D +D +S+RDMATQMSPE SP K R S + ST IVE Q H K VRDVQVDERVT+++W K K TG+GS + DDWKKKA E +S+ WEVS+TA + S KREEA+I AWENLQKAKAEA IRKLEMKLEKKRSSSM+KIM K ++A++KA++MRSS + S A Q + TSHK+ISFRRTR+ISSLSGCFTCHA
Sbjct: 3 PELGFQDQ-NQLRLGYR-TRDVSPDSVIFTPESNFTIFSSASGSVDRCSFASDVHDHESLASEFSQEHLAGHDLPESSS-GPDPDPNKSTVLKNSCLSKRVEKGKVQKEDNEAETKDGNQTLDSERSSFSQAIKECQDRRSRYEALLRRPDRRRPASLDLNNFITNATSSSPRFGVMKKNSVSNHQSGTCPSPGTPNYRHASVGIQKGWSSERVPLHANANRRHVGAAFLPFNNGRTLPSKWEDAERWIFSPIAGDGPARPSFPQPQRRQKSKSGPLGPPGIAYYSLYSPAVPMLEGGNVGNLMARSPFSAGVMVADGLSIQCGGGRGGGGGFPECMEPCMARSVSVHGCSELLSQSSLPGSQDEKLDGDKDAA------ISRRDMATQMSPELSP----KRRPSLSPSTPSAPSIVELQSIHSSKLEVRDVQVDERVTVTRWSKKHKARFTGKGSENVDDWKKKAAEARSSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAEIRKLEMKLEKKRSSSMDKIMNKLRSAQRKAQEMRSSVIASQAHQVARTSHKVISFRRTRRISSLSGCFTCHAF 569
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5J5AE72 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 625.165 bits (1611), Expect = 0.000e+0
Identity = 348/580 (60.00%), Postives = 419/580 (72.24%), Query Frame = 0
Match: A0A5J5AE72 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 625.165 bits (1611), Expect = 0.000e+0
Identity = 348/580 (60.00%), Postives = 419/580 (72.24%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFASESSQ---------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
MPELGFQH N SSG + ARDVSPDSV F+ ES+F FSSAS SV+RCSFAS+ Q LA H+ ESSS GPD PN+STV+KNS + V+K+KV+++D + E +DENQ LDSA +S SQALK+ Q RRSK+EALLK+SDRR P SLDLNN++TN TSSSPR GV+KK+ RPTGT PSPG P++ TS +QKGWSSERV L + NRRHV LP+NN RTLPSKWEDAERWIFSPV+GD R SF QP RRPK+KSGPLGPP AYYS+YSPAV + +GG V N M SPF+ G++ ADSLS+Q G F EP I RSVS+HGCS L QS + S D K + +D +IS VS+RDMATQMSPE SPH S + R S + ST L IVE Q H K VRDVQVDERVT+++W K + G+GS + D KKKA+E + + WEVS+TA + S KREEA+I AWENLQKAKAEAAI+KLE+KLEKKRSSSM+KI+ K ++A++KA+ MRSS + + A Q + TSHK+I FRRTRQISSLSGCFTCHA
Sbjct: 1 MPELGFQHQ-NQHSSG-NRARDVSPDSVTFTVESNFSLFSSASGSVDRCSFASDVHDHESLASEISQRLAGHDLLESSS-GPDPEPNKSTVHKNSRLIKRVEKAKVQKEDNEEEAEDENQTLDSAINSSSQALKERQDRRSKYEALLKRSDRRRPASLDLNNSITNATSSSPRFGVMKKNSVWARPTGTCPSPGTPSYRHTSVGVQKGWSSERVPLHNNANRRHVGTASLPFNNGRTLPSKWEDAERWIFSPVAGDGLVRHSFPQPQRRPKSKSGPLGPPGIAYYSLYSPAVPLLEGGNVGNLMAGSPFSAGMMVADSLSIQ---CGGGGGGFPACREPWIARSVSVHGCSELLSQSSMPGSQDEKLEGVKDAATDISCAVSRRDMATQMSPEGSPHPSPQRRPSLSPSTPSALSIVELQSVHSSKLEVRDVQVDERVTVTRWSKKHRAQFPGKGSENVDKCKKKAVEARPSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAAIQKLEVKLEKKRSSSMDKILNKLRSAQRKAQGMRSSVLANQAHQVARTSHKIIYFRRTRQISSLSGCFTCHAF 574
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2R6QXY5 ((Remorin, C-terminal protein isoform 1 {ECO:0000313|EMBL:PSS17254.1}))
HSP 1 Score: 619.387 bits (1596), Expect = 0.000e+0
Identity = 330/577 (57.19%), Postives = 410/577 (71.06%), Query Frame = 0
Match: A0A2R6QXY5 ((Remorin, C-terminal protein isoform 1 {ECO:0000313|EMBL:PSS17254.1}))
HSP 1 Score: 619.387 bits (1596), Expect = 0.000e+0
Identity = 330/577 (57.19%), Postives = 410/577 (71.06%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFASESSQ------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
M ELG + + S ARD SPDSVIF AES+F FSSAS SV RCSFAS+ QHLA + E+S GPD PN+ST + NS R+V+K+KV++++ E +++N+ LDSAR+SFSQ LK+CQ RRS+ E +LKKSDR P SLDLNN TN T++SPR GV+KK TR GT PSPG PN+ TS QKGWSSERV+L T+ NR+ VN LLP+NN RTLPSKWEDAERWIFSPVSGD RPS QP RRPK+KSGPLGPP AYYS+ SP + MF+GG + N M SPF+ V+ AD LS++ G G + +EPC+ RSVS+HGCS L S L D K D +DE +IS DVS+RDMATQMSPE S SS + + SF+ STS VL IV+ + K VRDVQVDERVTM++W K + +G+GS + D+WKKK LE +S++WEVS A N S KREEA++ AWENLQKAKAEAAIRKL+MKLEKKRSSSM++I+KK ++A+KKA++MR+S + + ++Q + TS+KLISFRR ISSLSGCFTCHA
Sbjct: 1 MAELGLEDRNQQISRFR--ARDFSPDSVIFIAESNFSLFSSASTSVNRCSFASDRDSLVSEVSQHLAGRDLRETSG-GPDSDPNKSTGHSNSCYRRKVEKAKVQKEENDEEIENKNETLDSARNSFSQPLKECQERRSRSENILKKSDRGRPASLDLNNHTTNATNASPRFGVMKKGSGSTRQIGTFPSPGTPNYRHTSIGAQKGWSSERVSLHTNGNRKQVNAALLPFNNGRTLPSKWEDAERWIFSPVSGDGPVRPSLQQPQRRPKSKSGPLGPPGVAYYSLCSPILPMFEGGNLGNLMAGSPFSARVLGADGLSIRSGAGS-GAGIYPAHLEPCMARSVSIHGCSELLSHSSLPGPQDGKIDENKDEATDISRDVSRRDMATQMSPEGSHQSSPRRKLSFSPSTSSVLSIVQLESVQPSKLEVRDVQVDERVTMTRWSKKHRVRFSGKGSENDDEWKKKDLEAESSSWEVSKAAKNISKMKREEAKVNAWENLQKAKAEAAIRKLKMKLEKKRSSSMDRIVKKLRSAQKKAQEMRNSVLTNQSRQVARTSNKLISFRRVPHISSLSGCFTCHAF 573
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7J0EK60 ((Remorin family protein {ECO:0000313|EMBL:GFY86855.1}))
HSP 1 Score: 619.002 bits (1595), Expect = 0.000e+0
Identity = 328/577 (56.85%), Postives = 411/577 (71.23%), Query Frame = 0
Match: A0A7J0EK60 ((Remorin family protein {ECO:0000313|EMBL:GFY86855.1}))
HSP 1 Score: 619.002 bits (1595), Expect = 0.000e+0
Identity = 328/577 (56.85%), Postives = 411/577 (71.23%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSFFSSASCSVERCSFASE---------SSQQHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHA 567
MPELGF+ N G RDVSPDSVIF+ FSSAS SV+RCSFAS+ + QHLA H+ E+SS GPD P +STV++NS +R+V K+KV ++D E D+N+ L SAR+S SQ+LK+CQ RRS+ E +LKK +R+ P SLDLNN +TN T SSPR GV+KKS A+TR TGT SPG PN S +QKGWSSERV L + NRRH + LLP+NN RTLPSKWEDAE+WIFSPVS D + +P F RRPK+KSGPLGPP AYYS++SP + M +GG V N SPF+ GVIAAD S++ + G F R+EPC+ RSVS+HG SG L QS L D K + +D NIS VS+RDMATQMSPE S HSS + R SF+ ST +LPIV+++ K VRDVQVDERVTM++W K + G+GS + D+WKKKA+E+QS+ WEVS+ A + S KREEA+I+AWE+LQ+AKAE+AIRKLEMKLEK RSSSM+KIM K ++ +KKA++MRSS + + ++Q S TS+K+ISF RTRQISSLSGCFTCHA
Sbjct: 1 MPELGFEDQ-NLLRPGFRN-RDVSPDSVIFT----IFSSASGSVDRCSFASDVHDHDSFASEASQHLAGHDLRETSS-GPDSDPKKSTVHRNSCLTRKVQKAKVHKEDIDAEIGDKNETLGSARNSLSQSLKECQDRRSRSEVVLKKPNRQRPASLDLNNHVTNATISSPRFGVMKKSSAMTRRTGTFLSPGTPNHRHASVGIQKGWSSERVPLHNNANRRHGSAALLPFNNGRTLPSKWEDAEKWIFSPVSADGAVKPPFQPQQRRPKSKSGPLGPPGIAYYSLHSPVLPMLEGGNVGNLDTVSPFSAGVIAADGFSIRSGVSSGGAGIFSTRIEPCMARSVSVHGFSGLLSQSLLPGPQDEKLNGDKDAATNISRAVSRRDMATQMSPEGSRHSSPRRRPSFSPSTPSILPIVKFESVQSSKLEVRDVQVDERVTMTRWSKKHRVRFPGKGSENVDNWKKKAIEVQSSAWEVSEAAKSISKMKREEAKISAWESLQRAKAESAIRKLEMKLEKSRSSSMDKIMNKLRSVQKKAQEMRSSVLTNQSRQVSKTSNKVISFHRTRQISSLSGCFTCHA 570
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2R6QY35 ((Remorin, C-terminal protein isoform 2 {ECO:0000313|EMBL:PSS17253.1}))
HSP 1 Score: 614.379 bits (1583), Expect = 0.000e+0
Identity = 330/579 (56.99%), Postives = 410/579 (70.81%), Query Frame = 0
Match: A0A2R6QY35 ((Remorin, C-terminal protein isoform 2 {ECO:0000313|EMBL:PSS17253.1}))
HSP 1 Score: 614.379 bits (1583), Expect = 0.000e+0
Identity = 330/579 (56.99%), Postives = 410/579 (70.81%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFASESSQ------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQS--PLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
M ELG + + S ARD SPDSVIF AES+F FSSAS SV RCSFAS+ QHLA + E+S GPD PN+ST + NS R+V+K+KV++++ E +++N+ LDSAR+SFSQ LK+CQ RRS+ E +LKKSDR P SLDLNN TN T++SPR GV+KK TR GT PSPG PN+ TS QKGWSSERV+L T+ NR+ VN LLP+NN RTLPSKWEDAERWIFSPVSGD RPS QP RRPK+KSGPLGPP AYYS+ SP + MF+GG + N M SPF+ V+ AD LS++ G G + +EPC+ RSVS+HGCS L S P D K D +DE +IS DVS+RDMATQMSPE S SS + + SF+ STS VL IV+ + K VRDVQVDERVTM++W K + +G+GS + D+WKKK LE +S++WEVS A N S KREEA++ AWENLQKAKAEAAIRKL+MKLEKKRSSSM++I+KK ++A+KKA++MR+S + + ++Q + TS+KLISFRR ISSLSGCFTCHA
Sbjct: 1 MAELGLEDRNQQISRFR--ARDFSPDSVIFIAESNFSLFSSASTSVNRCSFASDRDSLVSEVSQHLAGRDLRETSG-GPDSDPNKSTGHSNSCYRRKVEKAKVQKEENDEEIENKNETLDSARNSFSQPLKECQERRSRSENILKKSDRGRPASLDLNNHTTNATNASPRFGVMKKGSGSTRQIGTFPSPGTPNYRHTSIGAQKGWSSERVSLHTNGNRKQVNAALLPFNNGRTLPSKWEDAERWIFSPVSGDGPVRPSLQQPQRRPKSKSGPLGPPGVAYYSLCSPILPMFEGGNLGNLMAGSPFSARVLGADGLSIRSGAGS-GAGIYPAHLEPCMARSVSIHGCSELLSHSSLPGPQGTDGKIDENKDEATDISRDVSRRDMATQMSPEGSHQSSPRRKLSFSPSTSSVLSIVQLESVQPSKLEVRDVQVDERVTMTRWSKKHRVRFSGKGSENDDEWKKKDLEAESSSWEVSKAAKNISKMKREEAKVNAWENLQKAKAEAAIRKLKMKLEKKRSSSMDRIVKKLRSAQKKAQEMRNSVLTNQSRQVARTSNKLISFRRVPHISSLSGCFTCHAF 575
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B6Z7R9 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 613.609 bits (1581), Expect = 0.000e+0
Identity = 343/580 (59.14%), Postives = 410/580 (70.69%), Query Frame = 0
Match: A0A5B6Z7R9 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 613.609 bits (1581), Expect = 0.000e+0
Identity = 343/580 (59.14%), Postives = 410/580 (70.69%), Query Frame = 0
Query: 2 PELGFQHHSNSASSGLSGARDVSPDSVIFSAESSF--FSSASCSVERCSFAS----------ESSQQHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
PELGFQ N G RDVSPDSVIF+ ES+F FSSAS SV+RCSFAS E SQ+HLA H+ ESSS GPD PN+STV KNS S+ V+K KV+++D + ET D NQ LDS RSSFSQA+K+CQ RRS++EALL++ DRR P SLDLNN +TN TSSSPR GV+KK+ +GT PSPG PN+ S +QKGWSSERV L + NRRHV LP+NN RTLPSKWEDAERWIFSP++GD +RPSF QP RR K+KSGPLGPP AYYS+YSPAV M +GG V N M SPF+ GV+ AD LS+Q G G F + MEPC+ RSVS+HGCS L QS L S D K D +D +S+RDMATQMSPE SP K R S + ST IVE Q H K VRDVQVDERVT+++W K + G+GS + D+ KKK +E + + WEVS+TA + S KREEA+I AWENLQKAKAEAA+RKLEMKLEKKRSSSM+KI+ K ++A++KA+ MRSS + + A Q + TSHK+ISFRR RQISSLSGCFTCHA
Sbjct: 3 PELGFQDQ-NQLRLGYR-TRDVSPDSVIFTPESNFTIFSSASGSVDRCSFASDVHDHESLASEFSQEHLAGHDLPESSS-GPDPDPNKSTVLKNSCLSKRVEKGKVQKEDNEAETKDGNQTLDSERSSFSQAIKECQDRRSRYEALLRRPDRRRPASLDLNNFITNATSSSPRFGVMKKNSVSNHQSGTCPSPGTPNYRHASVGIQKGWSSERVPLHANANRRHVGAAFLPFNNGRTLPSKWEDAERWIFSPIAGDGPARPSFPQPQRRQKSKSGPLGPPGIAYYSLYSPAVPMLEGGNVGNLMARSPFSAGVMVADGLSIQCGGGRGGGGGFPECMEPCMARSVSVHGCSELLSQSSLPGSQDEKLDGDKDAA------ISRRDMATQMSPELSP----KRRPSLSPSTPSAPSIVELQSIHSSKLEVRDVQVDERVTVTRWSKKHRALFPGKGSENVDECKKKVVEARPSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAALRKLEMKLEKKRSSSMDKILNKLRSAQRKAQDMRSSVIANQAHQVARTSHKVISFRRARQISSLSGCFTCHAF 569
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: E0CPU6 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 608.601 bits (1568), Expect = 0.000e+0
Identity = 340/580 (58.62%), Postives = 417/580 (71.90%), Query Frame = 0
Match: E0CPU6 (Remorin_C domain-containing protein {ECO:0000259|Pfam:PF03763})
HSP 1 Score: 608.601 bits (1568), Expect = 0.000e+0
Identity = 340/580 (58.62%), Postives = 417/580 (71.90%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSFFSSASCS--VERCSFASESSQQ---------HLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHAL 568
M ELGFQ S GL GARD SPDSVIF+ ES+F +S S V+RCSFAS+ HLA H+ E+SS GPDL PN++TV+K+S R+ +K+KV ++D +VE ++EN VLDSAR+SFS ALK+CQ RRS+ EAL KK DRR P SLDLNN TSSSPR+G +KKS A +R +GT PSPG PN+ ++ +QKGWSSERV T+ NRRHV+ LLP+NN RTLPSKWEDAERWIFSPV+GD +PSF P RRPK+KSGPLGPP AYYS+YSPA+ MF+GG NFM SPF+ GVIA D L++ G RG R EPC+GRS S+HGCS L QS LR S D K D +D +IS VS+RD+ATQMSPE S SS + + SF+ S+ VLPIVE Q + K +RDVQVDERVTM++W K + G+GS + D WKKKA+E S+ WEVS+TA + S KREEA+I AWENLQKAKAEAAIRKLEMKLEKKRSSSM+KIM K ++A++KA++MRSS + + A Q S +HK +SF +TRQ+SSLSGCFTCHA
Sbjct: 1 MAELGFQDQS-LLRFGL-GARDASPDSVIFTQESNFSLFSSASASVDRCSFASDVHDHDSLASEVSLHLAGHDLQETSS-GPDLIPNKATVHKHSRLIRKEEKAKVLKEDKQVEAEEENLVLDSARNSFSLALKECQDRRSRSEALSKKHDRRRPASLDLNN----ATSSSPRLGGMKKSSASSRRSGTFPSPGTPNYRHSNFGIQKGWSSERVPSHTNVNRRHVSAALLPFNNGRTLPSKWEDAERWIFSPVAGDGVVKPSFPPPQRRPKSKSGPLGPPGIAYYSLYSPAIPMFEGGNAGNFMAGSPFSAGVIAPDGLAIH--CGGRGG-VMPVRTEPCMGRSASVHGCSELLNQSSLRDSRDEKFDGVKDAATDISRTVSRRDIATQMSPEGSIFSSPERKPSFSPSSPTVLPIVELQSVNSSKLEIRDVQVDERVTMTRWSKKHRGRIPGKGSENVDGWKKKAVEAHSSAWEVSETAKSISKVKREEAKITAWENLQKAKAEAAIRKLEMKLEKKRSSSMDKIMNKLRSAQRKAQEMRSSVLANHAHQVSGNAHKAVSFCKTRQMSSLSGCFTCHAF 570
BLAST of DCAR_008800 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2R6R3G5 ((Remorin, C-terminal protein {ECO:0000313|EMBL:PSS19748.1}))
HSP 1 Score: 607.831 bits (1566), Expect = 0.000e+0
Identity = 324/579 (55.96%), Postives = 411/579 (70.98%), Query Frame = 0
Match: A0A2R6R3G5 ((Remorin, C-terminal protein {ECO:0000313|EMBL:PSS19748.1}))
HSP 1 Score: 607.831 bits (1566), Expect = 0.000e+0
Identity = 324/579 (55.96%), Postives = 411/579 (70.98%), Query Frame = 0
Query: 1 MPELGFQHHSNSASSGLSGARDVSPDSVIFSAESSFFSSASCS--VERCSFASESSQ---------QHLAVHECGESSSSGPDLHPNESTVNKNSLKSREVDKSKVERKDTKVETDDENQVLDSARSSFSQALKDCQVRRSKFEALLKKSDRRTPTSLDLNNTLTNVTSSSPRIGVIKKSPAVTRPTGTLPSPGAPNFSQTSTVMQKGWSSERVALPTSTNRRHVNNVLLPYNNVRTLPSKWEDAERWIFSPVSGDSSSRPSFTQPHRRPKAKSGPLGPPRTAYYSMYSPAVHMFDGGIVENFMVASPFTPGVIAADSLSVQRDIGYRGNETFYDRMEPCIGRSVSLHGCSGTLCQSPLRSSDDRKHDTAEDEGKNISGDVSKRDMATQMSPEKSPHSSLKERHSFASSTSGVLPIVEWQDSHFPK-HVRDVQVDERVTMSQWCKNSKFHTTGEGSGHCDDWKKKALEIQSTNWEVSDTASNNSISKREEARIAAWENLQKAKAEAAIRKLEMKLEKKRSSSMEKIMKKFKAAEKKARKMRSSDVVSSAQQASTTSHKLISFRRTRQISSLSGCFTCHA 567
M ELG + + S ARD SPDSVIF+AES+F +S S V+RCSFAS++ QHLA + E+ GPDL PN+ST + NS R+V+K+KV++ + E +++++ LDSAR+SFSQALK+CQ RRS+ E +LKKSDRR P SLDLNN TN T++SPR GV+KK +TR TGT PSPG PN+ TS QKGWSSERV L T+ N + VN LLP+NN RTLPSKWEDAERWIFSPVSGD RPS QP RRPK+KSGPLGPP AYYS++SP + MF+GG N M SPF+ V+ AD LS++ G G + +EPC+ RSVS+HGCS + S L + K D +D NIS DVS+RDMATQMSPE SPHSS ++R SF+ STS VL I++ ++ K VRDVQVDERVTM++W K + +G+G + D+WKKK LE +S++WEVS+ A + S KREEA++ AWENLQ AKAEAAIRKLEMKLEKKRSSSM++IMKK ++A+KKA++MRSS + + + Q ++TS+K+ISFRR ISSL CFTCHA
Sbjct: 1 MAELGLEDRNQQISRFR--ARDFSPDSVIFTAESNFSLFSSASASVDRCSFASDAHDRDSLVSEISQHLAGRDLRETLG-GPDLDPNKSTGHINSCHRRKVEKAKVQKAENDSEIENKDETLDSARNSFSQALKECQERRSRSENILKKSDRRRPASLDLNNHTTNATNASPRFGVMKKGSGLTRQTGTFPSPGTPNYRHTSIGAQKGWSSERVPLHTNGNLKQVNPALLPFNNGRTLPSKWEDAERWIFSPVSGDGPVRPSLQQPQRRPKSKSGPLGPPGVAYYSLFSPVLPMFEGGNFGNLMAGSPFSAAVLGADGLSIRSGAGS-GAGIYPACLEPCMARSVSIHGCSELVSHSSLPGPQEWKIDENKDAATNISRDVSRRDMATQMSPEGSPHSSPRQRPSFSPSTSSVLSIMQSENVQSSKLEVRDVQVDERVTMTRWSKKHRVRFSGKGLENTDEWKKKDLEAESSSWEVSEAAKSISKLKREEAKVTAWENLQMAKAEAAIRKLEMKLEKKRSSSMDRIMKKLRSAQKKAQEMRSSVLTNQSHQVASTSNKVISFRRNSHISSLRSCFTCHA 575
| Match Name | Stats | Description |
|---|---|---|
| A0A5B6Z911 | E-Value: 0.000e+0, PID: 61.14 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| A0A5B6Z6L8 | E-Value: 0.000e+0, PID: 60.69 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| A0A5B6Z7B8 | E-Value: 0.000e+0, PID: 60.52 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| A0A5J5AE72 | E-Value: 0.000e+0, PID: 60.00 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| A0A2R6QXY5 | E-Value: 0.000e+0, PID: 57.19 | (Remorin, C-terminal protein isoform 1 {ECO:000031... [more] |
| A0A7J0EK60 | E-Value: 0.000e+0, PID: 56.85 | (Remorin family protein {ECO:0000313|EMBL:GFY86855... [more] |
| A0A2R6QY35 | E-Value: 0.000e+0, PID: 56.99 | (Remorin, C-terminal protein isoform 2 {ECO:000031... [more] |
| A0A5B6Z7R9 | E-Value: 0.000e+0, PID: 59.14 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| E0CPU6 | E-Value: 0.000e+0, PID: 58.62 | Remorin_C domain-containing protein {ECO:0000259|P... [more] |
| A0A2R6R3G5 | E-Value: 0.000e+0, PID: 55.96 | (Remorin, C-terminal protein {ECO:0000313|EMBL:PSS... [more] |
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back to topAnalysis:
| Name | Description |
|---|---|
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove these same DCAR gene predictions. | |
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins. Data from this analysis can be viewed in JBrowse here. |