MLQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLS
YICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQ
LGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNS
CIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCARTP
CTPSTLESLLVLVMKQCRCSKACYVLAPVRPMVLGPKRMSRGGTGVFLPW
HANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSDAEMIYKH*
| Relationships |
|---|
| The polypeptide, DCAR_004663, derives from mRNA, DCAR_004663. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A5A7P157 ((Oxidoreductase {ECO:0000313|EMBL:GER26523.1}))
HSP 1 Score: 278.87 bits (712), Expect = 3.035e-88
Identity = 164/336 (48.81%), Postives = 200/336 (59.52%), Query Frame = 0
Query: 3 QNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLV--GRLCARTPCTPSTLE-SLLVL------VMKQCRC------------------------------SKACYVLA----------PVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSDA 289
+ ++ICSNH+NCEAR + I +TKGFVAKEP+ ++ + + K +VNELR AGQNGELSG TFI+YNQ ++ GNKRE IQLG PIFG IKED + K+ IEPIP +LQGVI+HL+ WR I ENR PNSCII+FFDEGE+SQPFLKPPH+++P+ST LL ES MAFGRTLV G R S + SLLV+ + + C SKA V PV PMV+ P R R GTGVFLPW A +RKH K PPRAQ+GRFL+LPPPV + K E SD+
Sbjct: 177 ERVDICSNHDNCEARCSQIKITKGFVAKEPVNVVRGLKLYEDIFTDV-----ELSKLNDFVNELRSAGQNGELSGETFILYNQQRK----GNKRELIQLGVPIFGKIKEDEINTVQKNYIEPIPALLQGVIEHLIQWRLIPENRTPNSCIISFFDEGEYSQPFLKPPHLEQPLSTFLLHESTMAFGRTLVSYGEGNYRGSLMLSLNKGSLLVMKGNSSDMARHAMCSSLNKRTSITFFRVRTESENNHTSETNYSFSKAMSVWQPGVFLPWAHWPVGPMVVSPTRGPRDGTGVFLPW-AVESRKHAKQLPPRAQRGRFLALPPPVGSGKNESGSDS 502
Match: A0A5J5C9Z2 ((Uncharacterized protein {ECO:0000313|EMBL:KAA8550907.1}))
HSP 1 Score: 265.774 bits (678), Expect = 1.557e-84
Identity = 134/191 (70.16%), Postives = 152/191 (79.58%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLV 192
L++IEICSNHE+CEARR I MTKGFVAKEP+K HM + K+ + + K +VNELRVAGQNGELSG TFI+YNQ Q+KG NKRE IQLGAPIFG IKE+AT KS+IE IP +LQGVIDHL+ W ISENRKPNSCIINFFDEGE+SQPFLKPPH+D+PISTLLLSES MAFGRTLV
Sbjct: 186 LESIEICSNHEDCEARRTQIKMTKGFVAKEPVKGHMVNVVRGLKLYEDIFTDSELSKLTDFVNELRVAGQNGELSGETFILYNQ---QMKG-NKRELIQLGAPIFGQIKEEATSKHQKSHIERIPALLQGVIDHLIQWHLISENRKPNSCIINFFDEGEYSQPFLKPPHLDQPISTLLLSESTMAFGRTLV 372
Match: A0A5B6YM48 ((Uncharacterized protein {ECO:0000313|EMBL:MPA32446.1}) (Fragment))
HSP 1 Score: 269.626 bits (688), Expect = 3.183e-84
Identity = 143/229 (62.45%), Postives = 168/229 (73.36%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
L+NIEICSNHE+CEAR A I MTKGFVAKEP+K HM + K+ + + K +VN+LRVAGQNGELSG TFI+YNQ Q+KG NKRE IQLGAPIFG IKE+AT KS+IEPIP +L+GVIDHLV W ISENRKPNSCIINFFDEGE+SQPFLKPPH+D+PISTLLLSES MAFGRTL+ + P S L+ +LVM+ A +V+ P
Sbjct: 177 LENIEICSNHEDCEARHAQIKMTKGFVAKEPVKGHMVNVVRGLKLYEDIFTDSELSKLTDFVNDLRVAGQNGELSGETFILYNQ---QMKG-NKRELIQLGAPIFGQIKEEATSTYQKSHIEPIPALLEGVIDHLVQWHLISENRKPNSCIINFFDEGEYSQPFLKPPHLDQPISTLLLSESTMAFGRTLISDNDGNYKGPLMLS-LKEGSILVMRGNSADMARHVMCP 400
HSP 2 Score: 83.5741 bits (205), Expect = 2.210e-15
Identity = 41/66 (62.12%), Postives = 48/66 (72.73%), Query Frame = 0
Query: 223 CYVLAPVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSD 288
+LAPV+PMVL P+ + R GTGVFLPW G+RK KH PPRAQKGR L+LP PVE H E TS+
Sbjct: 471 VVMLAPVKPMVLSPRGIPRDGTGVFLPWTV-GSRKPAKHLPPRAQKGRLLALPSPVEAHVPEPTSN 535
Match: A0A5B6YKQ9 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471} (Fragment))
HSP 1 Score: 269.626 bits (688), Expect = 4.493e-84
Identity = 144/229 (62.88%), Postives = 167/229 (72.93%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
L+NIEICSNHE+CEAR A I MTKGFVAKEP+K HM + K+ + + K +VN+LRVAGQNGELSG TFI+YNQ Q+KG NKRE IQLGAPIFG IKE+AT KS+IEPIP +L+GVIDHLV W ISENRKPNSCIINFFDEGE+SQPFLKPPH+D+PISTLLLSES MAFGRTL+ + P S E L LVM+ A +V+ P
Sbjct: 180 LENIEICSNHEDCEARHAQIKMTKGFVAKEPVKGHMVNVVRGLKLYEDIFTDSELSKLTDFVNDLRVAGQNGELSGETFILYNQ---QMKG-NKRELIQLGAPIFGQIKEEATSTYQKSHIEPIPALLEGVIDHLVQWHLISENRKPNSCIINFFDEGEYSQPFLKPPHLDQPISTLLLSESTMAFGRTLISDNDGNYKGPLILSLKEGSL-LVMRGNSADMARHVMCP 403
HSP 2 Score: 72.7886 bits (177), Expect = 8.704e-12
Identity = 44/76 (57.89%), Postives = 51/76 (67.11%), Query Frame = 0
Query: 217 CRCSKACYVLAPVRPMVLGPKRMSRGGTG----VFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSD 288
R +LAPV+PMV+GPKR+ RGGTG VFLPW G+RK + PPRAQKGR L+LP PVE H E TSD
Sbjct: 472 LRAPVPVVMLAPVKPMVVGPKRIPRGGTGTGTGVFLPWTV-GSRKPARPLPPRAQKGRLLALPSPVEAHVPESTSD 546
Match: A0A5B6YLJ7 ((Uncharacterized protein {ECO:0000313|EMBL:MPA32445.1}) (Fragment))
HSP 1 Score: 268.855 bits (686), Expect = 6.630e-84
Identity = 143/229 (62.45%), Postives = 169/229 (73.80%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
L++IEICSNH++CEARRA I MTKGFVAKEP+K HM + K+ + + K +VN+LRVAGQNGELSG TFI+YNQ Q+KG NKRE IQLGAPIFG IKE+AT KS+IEPIP +L+GVIDHLV W ISENRKPNSCIINFFDEGE+SQPFLKPPH+D+PISTLLLSES MAFGRTLV + P S L+ +LVM+ A +V+ P
Sbjct: 178 LESIEICSNHDDCEARRAQIKMTKGFVAKEPVKGHMVNVVRGLKLYEEIFTDSELSKLTDFVNDLRVAGQNGELSGETFILYNQ---QMKG-NKRELIQLGAPIFGQIKEEATSTYQKSHIEPIPALLEGVIDHLVQWHLISENRKPNSCIINFFDEGEYSQPFLKPPHLDQPISTLLLSESMMAFGRTLVSDNDGNYKGPLMLS-LKEGSILVMRGNSADMARHVMCP 401
HSP 2 Score: 83.5741 bits (205), Expect = 2.363e-15
Identity = 41/67 (61.19%), Postives = 48/67 (71.64%), Query Frame = 0
Query: 223 CYVLAPVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSDA 289
+LAPV+PMVL P+ + R GTGVFLPW G+RK KH PPRAQKGR L+LP PVE H E TS+
Sbjct: 472 VVMLAPVKPMVLSPRGIPRDGTGVFLPWTV-GSRKPAKHLPPRAQKGRLLALPSPVEAHVPEPTSNT 537
Match: A0A7J7H4P3 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 263.848 bits (673), Expect = 4.899e-82
Identity = 140/229 (61.14%), Postives = 166/229 (72.49%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
++NI++CSNHE+CEARR I MTKGFVAKEP+K HM + K+ + + K +VNELRVAG+NGELSG ++I+YNQ Q+KG NKRE IQLGAPIFG IKE+AT KS IEPIP +LQGVIDHLV W ISENRKPNSCIINFFDEGEFSQPFLKPPH+D+PISTLLLSES MAFGRTL+ + P S L +LVM+ A +V+ P
Sbjct: 177 VENIDLCSNHEDCEARRDQIKMTKGFVAKEPVKGHMVNVVRGLKLYEDVFTNSELSKLNDFVNELRVAGRNGELSGESYILYNQ---QIKG-NKRELIQLGAPIFGQIKEEATTKHEKSYIEPIPTLLQGVIDHLVQWYLISENRKPNSCIINFFDEGEFSQPFLKPPHLDQPISTLLLSESAMAFGRTLISDNDGNYKGPLMLS-LNKGSLLVMRGNSSDMARHVMCP 400
HSP 2 Score: 89.7373 bits (221), Expect = 1.788e-17
Identity = 43/69 (62.32%), Postives = 50/69 (72.46%), Query Frame = 0
Query: 223 CYVLAPVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSDAEM 291
+LAP RPMVL PK + GGTGVFLPW G+RK KH PPRAQKGR L+LPPPVE H + TSD ++
Sbjct: 469 AIMLAPTRPMVLSPKTIPHGGTGVFLPWTV-GSRKPAKHLPPRAQKGRLLTLPPPVEMHILDPTSDPDI 536
Match: A0A5J5BKP0 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 260.381 bits (664), Expect = 9.837e-81
Identity = 138/229 (60.26%), Postives = 164/229 (71.62%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
L+N EICSNHE CEAR A I +TKGFVAKEP+K HM + K+ + + K +VNELRVAGQNGELSG TFI+YN+ + GNKRE IQLGAPIFG IKE+AT+ PK +IEPIP +LQGVI+HLV W +SENRKPNSCIINFFDEGE+SQPFLKPPH+D+PISTLLLSES MAFGRTL + P S L+ +LVM+ A +V+ P
Sbjct: 187 LENTEICSNHEECEARHAQIKITKGFVAKEPVKGHMVNVVRGLKLYEDIFTDSELSKLTDFVNELRVAGQNGELSGETFILYNRQTK----GNKRELIQLGAPIFGQIKEEATNTHPKCHIEPIPALLQGVINHLVQWHLLSENRKPNSCIINFFDEGEYSQPFLKPPHLDQPISTLLLSESTMAFGRTLTSDNDGNYKGPLILS-LKEGSILVMRGNSADMARHVMCP 410
Match: A0A7J0G1M5 ((Oxidoreductase, 2OG-Fe(II) oxygenase family protein {ECO:0000313|EMBL:GFZ04672.1}))
HSP 1 Score: 254.603 bits (649), Expect = 8.325e-79
Identity = 138/229 (60.26%), Postives = 160/229 (69.87%), Query Frame = 0
Query: 2 LQNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
+N ++CSNHE+CEARRA I MTKGFVAKE +K +M + K+ + + K +VNELRVAGQNGELSG TFI+YNQ K+ GNKRE IQLGA IFG IK +AT S+IEPIP +LQG IDHLV W ISENRKPNSCIINFFDEGEFSQPFLKPPH+D+PISTLLLSES MAFGRTLV + P S E LV VM+ A +V+ P
Sbjct: 165 FENEDLCSNHEDCEARRALIKMTKGFVAKEHVKGNMVNVVRGLKLYEDIFTDSELSKLNGFVNELRVAGQNGELSGETFILYNQKKK----GNKRELIQLGASIFGHIKGEATSEREDSHIEPIPTLLQGFIDHLVQWNLISENRKPNSCIINFFDEGEFSQPFLKPPHVDQPISTLLLSESTMAFGRTLVSDSDGNYKGPLMLSLKEGSLV-VMRGNSSDMARHVMCP 388
HSP 2 Score: 53.9138 bits (128), Expect = 1.433e-5
Identity = 23/38 (60.53%), Postives = 30/38 (78.95%), Query Frame = 0
Query: 225 VLAPVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHP 262
++AP+RPMV+ P+R+ GGTGVFLPW G+RK KHP
Sbjct: 456 MMAPMRPMVMSPRRIPHGGTGVFLPWGV-GSRKPAKHP 492
Match: A0A2R6QDQ4 ((Oligopeptide transporter like {ECO:0000313|EMBL:PSS06258.1}))
HSP 1 Score: 254.218 bits (648), Expect = 2.412e-78
Identity = 138/228 (60.53%), Postives = 160/228 (70.18%), Query Frame = 0
Query: 3 QNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLVGRLCA--RTPCTPSTLESLLVLVMKQCRCSKACYVLAP 228
+N ++CSNHE+CEARRA I MTKGFVAKE +K +M + K+ + + K +VNELRVAGQNGELSG TFI+YNQ K+ GNKRE IQLGA IFG IK +AT S+IEPIP +LQG IDHLV W ISENRKPNSCIINFFDEGEFSQPFLKPPH+D+PISTLLLSES MAFGRTLV + P S E LV VM+ A +V+ P
Sbjct: 186 ENEDLCSNHEDCEARRALIKMTKGFVAKEHVKGNMVNVVRGLKLYENIFTDSELSKLNGFVNELRVAGQNGELSGETFILYNQKKK----GNKRELIQLGASIFGHIKGEATSEREDSHIEPIPTLLQGFIDHLVQWNLISENRKPNSCIINFFDEGEFSQPFLKPPHVDQPISTLLLSESTMAFGRTLVSDSDGNYKGPLILSLKEGSLV-VMRGNSSDMARHVMCP 408
HSP 2 Score: 82.8037 bits (203), Expect = 3.711e-15
Identity = 40/67 (59.70%), Postives = 49/67 (73.13%), Query Frame = 0
Query: 225 VLAPVRPMVLGPKRMSRGGTGVFLPWHANGTRKHTKHPPPRAQKGRFLSLPPPVETHKTEVTSDAEM 291
++AP+RPMV+ P+R+ GGTGVFLPW G+RK KH PPRAQK R L+LP VE H E TSD +M
Sbjct: 476 MMAPMRPMVISPRRIPHGGTGVFLPWGV-GSRKPAKHLPPRAQKKRLLALPLAVERHIAESTSDPDM 541
Match: M1BSB3 ((Oxidoreductase {ECO:0000313|EnsemblPlants:PGSC0003DMT400051842}))
HSP 1 Score: 247.284 bits (630), Expect = 7.527e-78
Identity = 124/190 (65.26%), Postives = 147/190 (77.37%), Query Frame = 0
Query: 3 QNIEICSNHENCEARRAPINMTKGFVAKEPMKWHMASSFFQKKIESLSYICRHIRKEIYYVNELRVAGQNGELSGATFIMYNQAKQQVKGGNKRESIQLGAPIFGPIKEDATDHCPKSNIEPIPDILQGVIDHLVMWRWISENRKPNSCIINFFDEGEFSQPFLKPPHIDKPISTLLLSESEMAFGRTLV 192
+++E CSNHENCEAR A I MTKGFV+KEP+K HM + K+ + I K VNELR AGQNG+LSG TFI++NQ QVKG NKRE IQLG PIFG IKE+A C KSNIEPIP +LQGVIDHL+ W ISE+R+PNSC+IN+FDEGE+SQPF+KPPH+D+P+STLLLSES MAFGR LV
Sbjct: 158 ESVEFCSNHENCEARHAHIKMTKGFVSKEPVKGHMVNVVRGLKLFEDIFTPNEISKLNDLVNELRFAGQNGDLSGETFILFNQ---QVKG-NKREMIQLGTPIFGHIKEEAM--CQKSNIEPIPALLQGVIDHLIQWNLISESRRPNSCVINYFDEGEYSQPFMKPPHLDQPVSTLLLSESMMAFGRALV 341
| Match Name | Stats | Description |
|---|---|---|
| A0A5A7P157 | E-Value: 3.035e-88, PID: 48.81 | (Oxidoreductase {ECO:0000313|EMBL:GER26523.1})[more] |
| A0A5J5C9Z2 | E-Value: 1.557e-84, PID: 70.16 | (Uncharacterized protein {ECO:0000313|EMBL:KAA8550... [more] |
| A0A5B6YM48 | E-Value: 3.183e-84, PID: 62.45 | (Uncharacterized protein {ECO:0000313|EMBL:MPA3244... [more] |
| A0A5B6YKQ9 | E-Value: 4.493e-84, PID: 62.88 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A5B6YLJ7 | E-Value: 6.630e-84, PID: 62.45 | (Uncharacterized protein {ECO:0000313|EMBL:MPA3244... [more] |
| A0A7J7H4P3 | E-Value: 4.899e-82, PID: 61.14 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A5J5BKP0 | E-Value: 9.837e-81, PID: 60.26 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A7J0G1M5 | E-Value: 8.325e-79, PID: 60.26 | (Oxidoreductase, 2OG-Fe(II) oxygenase family prote... [more] |
| A0A2R6QDQ4 | E-Value: 2.412e-78, PID: 60.53 | (Oligopeptide transporter like {ECO:0000313|EMBL:P... [more] |
| M1BSB3 | E-Value: 7.527e-78, PID: 65.26 | (Oxidoreductase {ECO:0000313|EnsemblPlants:PGSC000... [more] |
Pages
back to top| 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. |