DCAR_028090

Resource Type: 
Polypeptide
Name: 
DCAR_028090
Identifier: 
DCAR_028090.mRNA-protein
Sequence: 
MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTY
RLNPTFQKNLQNHILHGGVLPREPMKINVRLPSSADLDAYASGQWESFLL
HLISSTEAEATRNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTN
AQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQG
SIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVE
TNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGIT
SDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYD
EFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQNAF
DLFKRPRQREITEEEQEPVELLMMSLRNLF*
Sequence Length: 
431
Sequence Checksum: 
c7d2dd71d5265b494364023f7d145efc
View location in JBrowse: 
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, DCAR_028090, derives from mRNA, DCAR_028090.
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Blast Results: 
The following BLAST results are available for this feature:
BLAST of DCAR_028090 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
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6L2KPF7 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 667.152 bits (1720), Expect = 0.000e+0
Identity = 312/398 (78.39%), Postives = 355/398 (89.20%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPMKIN--VRLPSSADLDAYASGQWESFLLHLISSTEAEAT-RNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFL 395
            +LYI  P+  +S++ WV A+G SKHRVA+D+L+QLR+FTETVDRK+E TYRLNP FQ NL+ HI+HGGVLPREPM  N  VRLPS  +LD Y++ QWE FLLHLI+S EAEAT ++IS+SMMK+FQRGLLSQRDRE  +LTESGFQFLLMDTNAQLWY+IREYI++ E+RGVD++DLISFLLELSFHV+GEAYN+NTL   Q + VKDLADLGL+KLQQG K+SWFIPTKLA NLSISLSDASSRKQGYVVVETNFRLYAY+TSKLHCEIL+LF+R+EYQLPNLIVG+ITKENLYKAF NGITSDQII FLQQNAHPRVAE+VPSVPENVTDQIRLWESDLNRVEMTP+H +D+FPSRD FEAACDFAREY  LLWEDS KMR+IVK E Y HMK FL
Sbjct:   51 LLYIDVPVTASSLQEWVLADGASKHRVAVDRLIQLRVFTETVDRKKEATYRLNPMFQMNLREHIVHGGVLPREPMAANITVRLPSLEELDNYSAQQWECFLLHLINSAEAEATTKSISASMMKVFQRGLLSQRDREGALLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDSADLISFLLELSFHVTGEAYNINTLDDIQRTTVKDLADLGLIKLQQGRKDSWFIPTKLATNLSISLSDASSRKQGYVVVETNFRLYAYSTSKLHCEILKLFSRVEYQLPNLIVGSITKENLYKAFANGITSDQIISFLQQNAHPRVAERVPSVPENVTDQIRLWESDLNRVEMTPAHFFDDFPSRDVFEAACDFAREYSSLLWEDSKKMRLIVKTELYAHMKEFL 448    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7J7GYB8 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 665.226 bits (1715), Expect = 0.000e+0
Identity = 313/400 (78.25%), Postives = 354/400 (88.50%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISS-TEAEATRNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            MLYI  P+   SM+ WV A+G SKH VAID+L+QLRLFTE VDRK+ETTYRLNPTFQ NLQ HI+HGGVLPREPM   I VRLPS  DLDAYA+ QWE FLLHLISS T+ E T N SSS+MKIFQRGLLSQRD+E P LTESGFQFLLMDTNAQLWY+IREYIT+ EERG+D++DLISF+LELSFHV+GEAYNMNTL+ SQ +++KDLADLGLVKLQQG KESWFIPTKLA NLSISLSD SSRK G+VVVETNFR+YAY+TSKLHCEILRLF+R+EYQLPNLIV AITKENLY AF+NGI ++QII FLQQNAHPRVAE+VPSVPENVTDQIRLWESD+NRVE+TP+H YDEFP+R+ F+AACDFAREYGGLLWEDS  MR++VKAE   HM+ FLR+
Sbjct:   51 MLYIDVPVSAKSMQEWVLADGYSKHNVAIDRLIQLRLFTEAVDRKKETTYRLNPTFQINLQKHIIHGGVLPREPMPSNITVRLPSLEDLDAYAAEQWECFLLHLISSSTQGEKTTNFSSSLMKIFQRGLLSQRDKEPPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGLDSADLISFMLELSFHVTGEAYNMNTLTDSQRNVIKDLADLGLVKLQQGRKESWFIPTKLATNLSISLSDTSSRKLGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVAAITKENLYNAFENGIMAEQIISFLQQNAHPRVAERVPSVPENVTDQIRLWESDMNRVEITPAHFYDEFPTREVFDAACDFAREYGGLLWEDSKTMRLVVKAEILMHMRDFLRR 450    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2U1LYY2 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 662.529 bits (1708), Expect = 0.000e+0
Identity = 311/398 (78.14%), Postives = 351/398 (88.19%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPMKIN--VRLPSSADLDAYASGQWESFLLHLISSTEAEAT-RNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFL 395
            +LYI  P+   S++ WV A+G SKHRVA+D+L+QLR+FTETVDRK+E TYRLNP FQ NL+ HI+HGGVLPREPM  N  VRLPS  +LD YA+ QWE FLLHLI+S EAE T ++IS+SMMK+FQRGLLSQRDRE   LTESGFQFLLMDTNAQLWY+IREYI++ E+RGVD++DLISFLLELSFHV+GEAYN+NTL   Q + VKDLADLGL+KLQQG K+SWFIPTKLA NLSISLSDASSRKQGYVVVETNFRLYAY+TSKLHCEIL+LF+R+EYQLPNLIVG+ITKENLYKAF NGIT+DQII FLQQNAHPRVAE+VPSVPENVTDQIRLWESDLNRVEMTP+H  D+FPSRD FEAACDFAREY  LLWEDS KMR+IVK E Y HMK FL
Sbjct:   51 LLYIDVPVTANSLQEWVLADGASKHRVAVDRLIQLRVFTETVDRKKEATYRLNPMFQMNLREHIVHGGVLPREPMAANITVRLPSLEELDNYAAQQWECFLLHLINSAEAEVTTKSISASMMKVFQRGLLSQRDREGSRLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDSADLISFLLELSFHVTGEAYNINTLDDVQRTTVKDLADLGLIKLQQGRKDSWFIPTKLATNLSISLSDASSRKQGYVVVETNFRLYAYSTSKLHCEILKLFSRVEYQLPNLIVGSITKENLYKAFANGITADQIISFLQQNAHPRVAERVPSVPENVTDQIRLWESDLNRVEMTPAHFLDDFPSRDVFEAACDFAREYSSLLWEDSKKMRLIVKTEIYAHMKEFL 448    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2G9IAI3 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 661.759 bits (1706), Expect = 0.000e+0
Identity = 307/400 (76.75%), Postives = 356/400 (89.00%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRD-REAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            +LYI  P+    +E WV  +G+SKH+VAID+L+QLR+ TETV+RK+ETTY  NPTFQ+NLQ HI+HGG+LPREPM   I VRLPS  +LDAYA+ QWE FLLHLI+S E E + NI SSMMK+FQRGLLSQRD +E P LTESGFQFLLMDTNAQLWY++REYIT+CE+ GVDT+DLISFLLELSFHV+G+AYN+NTLS  Q +I+KDLADLGLVKLQQG KESWFIPTKLA NLSISL+D SSRKQG+VVVETNFR+YAY+TSKLHCEILRLF+RIEYQLPNLIVGAITKE+LYKAFQNGIT++QI+ FLQQNAHPRVAE++P+VPENVTDQIRLWESDLNRVEM P+HLYDEFPSR+ FEAACDFAREYGGLLWE+S KMR++VKAE +  MK FLR+
Sbjct:   51 LLYIEGPVTAKWLEEWVLPDGVSKHKVAIDRLIQLRVLTETVERKKETTYLFNPTFQRNLQKHIVHGGILPREPMPSNITVRLPSLEELDAYAAQQWELFLLHLINSAEVEKSTNIRSSMMKVFQRGLLSQRDEKEPPKLTESGFQFLLMDTNAQLWYIVREYITNCEDHGVDTADLISFLLELSFHVTGQAYNLNTLSDIQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSISLADTSSRKQGFVVVETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYKAFQNGITAEQIVSFLQQNAHPRVAERIPTVPENVTDQIRLWESDLNRVEMAPAHLYDEFPSREVFEAACDFAREYGGLLWENSKKMRLVVKAEIFTQMKEFLRR 450    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A5BMX1 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 659.062 bits (1699), Expect = 0.000e+0
Identity = 306/400 (76.50%), Postives = 354/400 (88.50%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQN 398
            MLYI  P+   +ME WV A+G SKHRVAID+L+QLR+FTET DRK+ET+YRLNPTFQ NLQ H+++GGVLPREPM   I VRLPS  DL+AYA GQWE FLL LISST+ E   N SSS+MK+FQRGLL+QR++EAP LTESGFQFLLMDTNAQLWY++REYI++ EERGVD +DLISFLLELSFHV+GEAYN+NTL+  Q + +KDL DLGLVKLQQG KESWFIPTKLA NLS+SLSD SSRKQG+VVVETNFRLYAY++SKLHCEILRLF+R+EYQLPNLIVGAITKE+LY AF+NGIT++QII FLQQNAHPRVAE+ P+VPENVTDQIRLWE+DLNRVE  PSHLYDEFPSRD FEAACDFAREYGGLLWEDS KMR++VKAE + HM+ +LR++
Sbjct:   51 MLYIDVPVTAKAMEEWVLADGFSKHRVAIDRLIQLRVFTETSDRKKETSYRLNPTFQTNLQKHLIYGGVLPREPMPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFSSSLMKVFQRGLLTQREKEAPRLTESGFQFLLMDTNAQLWYIMREYISNSEERGVDPADLISFLLELSFHVTGEAYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKLATNLSMSLSDTSSRKQGFVVVETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLHMREYLRRS 450    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A830D7S9 ((General transcription factor iih subunit 4 {ECO:0000313|EMBL:GFQ06703.1}))

HSP 1 Score: 658.292 bits (1697), Expect = 0.000e+0
Identity = 311/400 (77.75%), Postives = 354/400 (88.50%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRDREAPM-LTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            +LYI  P+ +  +E WV  +G+SKHRVA+D+L+QLR+ TETVDRK+ETTY +N TFQ NLQ HI+HGGVLPREPM   I VRLPS  DLDAYA  QWE FLLHLI+S+EAE + NISSSMMKIFQRGLLSQ+D + P  LTESGFQFLLMDTNAQLWY++REYIT+CEE GVDT+DLISFLLELSFHV+G+AYN+NTLS  Q SIVKDL DLGLVKLQQG KESWFIPTKLA NLSISL+D SSRK+GYVVVETNFR+YAY+TSKLHCEILRLF+RIEYQLPNLIVGAITKE+L KAF NGIT++QI+ FLQQNAHPRVAE++PSVPENVTDQIRLWE+DLNRVEMTP+HLYDEFPSRD FEAACDFAREYGGLLWE+S KMR++VK E +  MK FLR+
Sbjct:   51 LLYIDGPVSSKLLEEWVLPDGVSKHRVAVDRLIQLRVLTETVDRKKETTYLVNRTFQHNLQKHIVHGGVLPREPMPSNITVRLPSLEDLDAYAVQQWELFLLHLINSSEAEKSTNISSSMMKIFQRGLLSQKDDKEPAKLTESGFQFLLMDTNAQLWYIVREYITNCEEHGVDTADLISFLLELSFHVTGKAYNLNTLSDRQRSIVKDLTDLGLVKLQQGRKESWFIPTKLATNLSISLADTSSRKEGYVVVETNFRVYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLNKAFLNGITAEQIVSFLQQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEMTPAHLYDEFPSRDVFEAACDFAREYGGLLWENSKKMRIVVKGEIFTQMKEFLRR 450    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1S4AUE0 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 656.751 bits (1693), Expect = 0.000e+0
Identity = 311/400 (77.75%), Postives = 351/400 (87.75%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRD-REAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            +LYI  PI   SME WV  +G SKH+VAID+L+QLR+ TET DRK+E  YRLNP FQ NLQ HI+HGGVLPREPM   I VRLPS  +L+A+A  QWE FLLHLISS+EA  T NISSSMMKIFQRGLLSQRD RE P LTESGFQFLLMDTNAQLWY+IREYIT+ EERGVD++DLI+FLLELSFHV+G+AYN NTL+  Q SI KDL+DLGLVKLQQG KESWFIPTKLA NLSISL+D +SRKQG++V+ETNFRLYAY+TSKLHCEILRLFAR+EYQLPNLIVGAITKE+LYKAFQNGIT++QII FLQQNAHPRVAE++PSVPENVTDQIRLWESDLNRVEM P+HLYDEFPS+D FEAACDFAREYGGLLWEDS ++R+IVKA+    MK FLR+
Sbjct:   51 LLYIDIPISAKSMEEWVLPDGFSKHKVAIDRLIQLRVMTETFDRKKEAMYRLNPKFQFNLQKHIVHGGVLPREPMPSNITVRLPSLEELEAFAVEQWECFLLHLISSSEAGKTTNISSSMMKIFQRGLLSQRDDREPPRLTESGFQFLLMDTNAQLWYIIREYITNAEERGVDSADLIAFLLELSFHVTGKAYNTNTLTDLQRSITKDLSDLGLVKLQQGRKESWFIPTKLATNLSISLADTTSRKQGFIVIETNFRLYAYSTSKLHCEILRLFARVEYQLPNLIVGAITKESLYKAFQNGITAEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVEMIPAHLYDEFPSKDVFEAACDFAREYGGLLWEDSKQLRIIVKADILTEMKEFLRR 450    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1S4AV23 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 655.596 bits (1690), Expect = 0.000e+0
Identity = 311/400 (77.75%), Postives = 351/400 (87.75%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRD-REAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            +LYI  PI   SME WV  +G SKH+VAID+L+QLR+ TET DRK+E  YRLNP FQ NLQ HI+HGGVLPREPM   I VRLPS  +L+A+A  QWE FLLHLISS+EA  T NISSSMMKIFQRGLLSQRD RE P LTESGFQFLLMDTNAQLWY+IREYIT+ EERGVD++DLI+FLLELSFHV+G+AYN NTL+  Q SI KDL+DLGLVKLQQG KESWFIPTKLA NLSISL+D +SRKQG++V+ETNFRLYAY+TSKLHCEILRLFAR+EYQLPNLIVGAITKE+LYKAFQNGIT++QII FLQQNAHPRVAE++PSVPENVTDQIRLWESDLNRVEM P+HLYDEFPS+D FEAACDFAREYGGLLWEDS ++R+IVKA+    MK FLR+
Sbjct:   27 LLYIDIPISAKSMEEWVLPDGFSKHKVAIDRLIQLRVMTETFDRKKEAMYRLNPKFQFNLQKHIVHGGVLPREPMPSNITVRLPSLEELEAFAVEQWECFLLHLISSSEAGKTTNISSSMMKIFQRGLLSQRDDREPPRLTESGFQFLLMDTNAQLWYIIREYITNAEERGVDSADLIAFLLELSFHVTGKAYNTNTLTDLQRSITKDLSDLGLVKLQQGRKESWFIPTKLATNLSISLADTTSRKQGFIVIETNFRLYAYSTSKLHCEILRLFARVEYQLPNLIVGAITKESLYKAFQNGITAEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVEMIPAHLYDEFPSKDVFEAACDFAREYGGLLWEDSKQLRIIVKADILTEMKEFLRR 426    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B6ZSH0 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 654.825 bits (1688), Expect = 0.000e+0
Identity = 318/398 (79.90%), Postives = 357/398 (89.70%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRDREAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLR 396
            MLYI  PI   SME WV A+G SKH+VAID+L+QLRL TETVDRK+ET+YRLN TFQ NLQ HI+HGGVLPREPM   I VRLPS  DL+AYAS QWESFLLHLISS++AE   N SSSMMKIFQRGLLSQRD+EAP LTESGFQFLLMDTNAQLWY++REYIT+ EERGVD++DLISFLLELSFHV+GEAYN+NTL+  Q +  KDLADLGLVKLQQG KESWFIPTKLA NLSISLSD+SSRKQG+VVVETNFR+YAY+TSKLHCEILRLF+RIEYQLPNLIVGAITKE+LY AF+NGIT++QII FLQQNAHPRVAE++PSV ENVTDQIRLWESD+NRVEMTP+HL DEFPSRD FEAACDFAREYGG+LWEDS +MR++VKAE + HM+ FLR
Sbjct:   51 MLYIDVPISAKSMEEWVLADGFSKHKVAIDRLIQLRLLTETVDRKKETSYRLNSTFQINLQKHIVHGGVLPREPMPSNITVRLPSLDDLEAYASEQWESFLLHLISSSQAERMTNFSSSMMKIFQRGLLSQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYITNSEERGVDSADLISFLLELSFHVTGEAYNLNTLTDFQRNATKDLADLGLVKLQQGRKESWFIPTKLATNLSISLSDSSSRKQGFVVVETNFRIYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAERIPSVTENVTDQIRLWESDMNRVEMTPAHLCDEFPSRDVFEAACDFAREYGGMLWEDSKQMRLVVKAEIHTHMREFLR 448    
BLAST of DCAR_028090 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6N2BRN4 (RNA polymerase II transcription factor B subunit 2 {ECO:0000256|RuleBase:RU364024})

HSP 1 Score: 654.055 bits (1686), Expect = 0.000e+0
Identity = 308/400 (77.00%), Postives = 351/400 (87.75%), Query Frame = 0
 
Query:    1 MLYIIEPIVTTSMEAWVAAEGMSKHRVAIDKLVQLRLFTETVDRKRETTYRLNPTFQKNLQNHILHGGVLPREPM--KINVRLPSSADLDAYASGQWESFLLHLISSTEAEATRNISSSMMKIFQRGLLSQRD-REAPMLTESGFQFLLMDTNAQLWYVIREYITHCEERGVDTSDLISFLLELSFHVSGEAYNMNTLSHSQGSIVKDLADLGLVKLQQGMKESWFIPTKLAINLSISLSDASSRKQGYVVVETNFRLYAYTTSKLHCEILRLFARIEYQLPNLIVGAITKENLYKAFQNGITSDQIICFLQQNAHPRVAEKVPSVPENVTDQIRLWESDLNRVEMTPSHLYDEFPSRDAFEAACDFAREYGGLLWEDSVKMRVIVKAETYDHMKRFLRQ 397
            MLYI  PI   SME WV  +G SKH+VAID+L+QLR+ TET DRK+E  Y+LNP FQ NLQ HI+HGGVLPREPM   I VRLPS  +L+AYA  QWE FLL+LISS+EA  T NISSSMMKIFQRGLLSQRD RE P LTESGFQFLLMDTNAQLWY+IREYIT+ EERGVD++DLI+FLLELSFHV+G+AYN NT++  Q SI+KDL+DLGLVKLQQG KESWFIPTKLA NLSISL+D ++RKQG++V+ETNFRLYAY+TSKLHCEILRLFAR+EYQLPNLIVGAI KE+LYKAFQNGITS+QI+ FLQQNAHPRVAE++PSVPENVTDQIRLWESDLNRVEMTP+H YDEFPS+D FEAACDFAREYGGLLWEDS +MR++VKA+    MK FLR+
Sbjct:   51 MLYIDIPITAKSMEEWVLPDGFSKHKVAIDRLIQLRVMTETFDRKKEAMYQLNPKFQFNLQKHIVHGGVLPREPMPSNITVRLPSLEELEAYAVEQWECFLLNLISSSEAGKTTNISSSMMKIFQRGLLSQRDDREPPRLTESGFQFLLMDTNAQLWYIIREYITNAEERGVDSADLIAFLLELSFHVTGKAYNTNTITDLQRSIIKDLSDLGLVKLQQGRKESWFIPTKLATNLSISLADTTTRKQGFIVIETNFRLYAYSTSKLHCEILRLFARVEYQLPNLIVGAINKESLYKAFQNGITSEQIVSFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVEMTPAHFYDEFPSKDVFEAACDFAREYGGLLWEDSKRMRLVVKADILAEMKEFLRR 450    
Match NameStatsDescription
A0A6L2KPF7E-Value: 0.000e+0, PID: 78.39RNA polymerase II transcription factor B subunit 2... [more]
A0A7J7GYB8E-Value: 0.000e+0, PID: 78.25RNA polymerase II transcription factor B subunit 2... [more]
A0A2U1LYY2E-Value: 0.000e+0, PID: 78.14RNA polymerase II transcription factor B subunit 2... [more]
A0A2G9IAI3E-Value: 0.000e+0, PID: 76.75RNA polymerase II transcription factor B subunit 2... [more]
A5BMX1E-Value: 0.000e+0, PID: 76.50RNA polymerase II transcription factor B subunit 2... [more]
A0A830D7S9E-Value: 0.000e+0, PID: 77.75(General transcription factor iih subunit 4 {ECO:0... [more]
A0A1S4AUE0E-Value: 0.000e+0, PID: 77.75RNA polymerase II transcription factor B subunit 2... [more]
A0A1S4AV23E-Value: 0.000e+0, PID: 77.75RNA polymerase II transcription factor B subunit 2... [more]
A0A5B6ZSH0E-Value: 0.000e+0, PID: 79.90RNA polymerase II transcription factor B subunit 2... [more]
A0A6N2BRN4E-Value: 0.000e+0, PID: 77.00RNA polymerase II transcription factor B subunit 2... [more]

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Analysis: 
NameDescription

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
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

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.

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