DCAR_009549

Resource Type: 
Polypeptide
Name: 
DCAR_009549
Identifier: 
DCAR_009549.mRNA-protein
Sequence: 
MAVPSAFAGPKLENIFLGNASHNGVVFCKPRKAVFPRNSTSLRCEQQQLQ
TTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHT
TPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQ
HRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVL
GEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGA
VSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMV
VVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLF
LKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKE
VVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERI
RLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDS
RTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQKCASQGAVSTTL
SLVVVNILVILKPCCLYWLPPCCQEDNIRGDDVLKQVNHIIFIANASSVP
ERQSLMVANIRLL*
Sequence Length: 
614
Sequence Checksum: 
41dd82653b3fd15a07518f91e8175da0
View location in JBrowse: 
DCARv2_Chr3:8779788..8783575+
Organism: 
Daucus carota subspecies sativus
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, DCAR_009549, derives from mRNA, DCAR_009549.
Blast Results: 
The following BLAST results are available for this feature:
BLAST of DCAR_009549 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
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7J7HRD1 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 895.96 bits (2314), Expect = 0.000e+0
Identity = 439/552 (79.53%), Postives = 482/552 (87.32%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLGNASHNGV---------VFCKP---RKAVFPRNSTSLRCEQQQLQTTNDNVIVD-NSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV SAFAG K+E++ L N   +           V CKP   R+A+  R   S+RCE          V+VD N      S SLSAL+QLK+SAADRYTKERSSIVVIGLS+HTTPVEMREKLA+PEAEWPRAI+ELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+P S++C+HRFLLYN DATQH+FEVSAGLDSLVLGEGQILAQVKQVVKVGQG+ GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++SHSTARML+IGAGKMGKLVIKHL AKGCTKMVVVNR+EERV AIREEL  +EIIY+PL++ML  AAEADVIFTSTASETPLFLKEHV D PPVG +VG +R FVDISVPRNVGSC+ +L+  RVYNVDDLKEVV+ANKEDRLRKA EAQ II EESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MGDD++KK ++A DDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLE EISVLEQK+RAKVEQNQK
Sbjct:    1 MAVSSAFAGAKVESLLLSNTGGSSSSLSRSSQIPVLCKPSRTRRALIQRGGLSIRCE------IVSEVLVDPNRASVSPSPSLSALEQLKASAADRYTKERSSIVVIGLSVHTTPVEMREKLAVPEAEWPRAIAELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPVSEICQHRFLLYNKDATQHLFEVSAGLDSLVLGEGQILAQVKQVVKVGQGITGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESSHSTARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRTEERVAAIREELKDVEIIYQPLSEMLPCAAEADVIFTSTASETPLFLKEHVMDFPPVGQEVGGLRHFVDISVPRNVGSCVTDLDATRVYNVDDLKEVVAANKEDRLRKAMEAQAIITEESKQFEAWRDSLETVPTIKKLRAYAERIRVAELEKCLSKMGDDISKKARRAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLETEISVLEQKIRAKVEQNQK 546
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6J1K420 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 891.338 bits (2302), Expect = 0.000e+0
Identity = 437/547 (79.89%), Postives = 487/547 (89.03%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLGNASHNGV----VFCKP---RKAVFPRNS-TSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV ++F+G KLE + L +A+ +      +FCK    R+  F R+  +SLRCE      ++D ++ ++      SS+LSAL+QLK+SAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAI ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+P S++C+HRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP+ SH+TARML+IGAGKMGKLVIKHL AKGCTKMVVVNRSEERVTAIREE+  +EIIYKPLT+ML+ AAEADVIFTSTASE+ LF KE V +LPPVG DVG +RLF+DISVPRNVG+CI +LE  RVYNVDDLKEVV+ANKEDRLRKA EAQ+II EESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MGDD+ KKT++A DDLSRGIVNKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMFSLE EI+VLEQK+RAKVEQNQK
Sbjct:    1 MAVSTSFSGTKLEALLLKSAATSSFSHLPLFCKSIRSRRIPFQRSEFSSLRCEV----ASSDVLVQNDEIDRAKSSNLSALEQLKTSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAIGELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPVSEICQHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVAGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPEPSHATARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEERVTAIREEIKDVEIIYKPLTEMLSCAAEADVIFTSTASESLLFTKEEVKNLPPVGHDVGDLRLFLDISVPRNVGACINDLENVRVYNVDDLKEVVAANKEDRLRKAMEAQSIITEESKQFEAWRDSLETVPTIKKLRAYAERIRMAELEKCLSKMGDDIPKKTRRAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFSLETEIAVLEQKIRAKVEQNQK 543
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6J1BVE9 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 890.567 bits (2300), Expect = 0.000e+0
Identity = 434/553 (78.48%), Postives = 489/553 (88.43%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFL-------GNASHNGVVFC---KPRKAVFPRNS----TSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV ++F+G KLE + L       G++S    VFC   + R+  F R      T +RCE   + +++D ++ ++     ++S+LSAL+QLK+SAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAI ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSK+SG+P S++C+HRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP+TSH++A+ML+IGAGKMGKLVIKHL AKGCTKMVVVNRSEERVTAIREE+  +EIIYKPLT+M+++AAEADVIFTSTASE+ LF KE V DLPPVG DVG +RLF+DISVPRNVG+CI +LE  RVYNVDDLKEVV+ANKEDRLRKA EAQ+II EESKQF AWRDSLETVPTIKKLRAYAERIR AEL+KCLS+MGDD+ KKT++A DDLSRGIVNKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMFSLE EI+VLEQK+RAKVEQNQK
Sbjct:    1 MAVSTSFSGAKLEALLLKSAATSRGSSSSQLPVFCNSIRSRRVQFHRTGFPSFTPVRCE---VASSSDVLVQNDEIDRATASNLSALEQLKTSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAIGELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKSSGIPVSEICQHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVAGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPETSHASAKMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEERVTAIREEIEDVEIIYKPLTEMISSAAEADVIFTSTASESLLFTKEQVKDLPPVGHDVGGLRLFIDISVPRNVGACINDLEDVRVYNVDDLKEVVAANKEDRLRKAMEAQSIITEESKQFEAWRDSLETVPTIKKLRAYAERIRTAELEKCLSKMGDDIPKKTRRAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFSLETEIAVLEQKIRAKVEQNQK 550
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6J1HDK8 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 889.412 bits (2297), Expect = 0.000e+0
Identity = 436/547 (79.71%), Postives = 487/547 (89.03%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLGNASHNGV----VFCKP---RKAVFPRNS-TSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV ++F+G KLE + L +A+ +      +FCK    ++  F R+  +SLRCE      ++D ++ ++      SS+LSAL+QLK+SAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAI ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+P S++C+HRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP+ SH+TARML+IGAGKMGKLVIKHL AKGCTKMVVVNRSEERVTAIREE+  +EIIYKPLT+ML+ AAEADVIFTSTASE+ LF KE V +LPPVG DVG +RLF+DISVPRNVG+CI +LE  RVYNVDDLKEVV+ANKEDRLRKA EAQ+II EESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MGDD+ KKT++A DDLSRGIVNKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMFSLE EI+VLEQK+RAKVEQNQK
Sbjct:    1 MAVSTSFSGAKLEALLLKSAATSSSSHLPLFCKSIRSKRIPFQRSGFSSLRCEV----ASSDVLVQNDEIDRAKSSNLSALEQLKTSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAIGELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPVSEICQHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVAGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPEPSHATARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEERVTAIREEIKDVEIIYKPLTEMLSCAAEADVIFTSTASESLLFTKEEVKNLPPVGHDVGGLRLFLDISVPRNVGACINDLENVRVYNVDDLKEVVAANKEDRLRKAMEAQSIITEESKQFEAWRDSLETVPTIKKLRAYAERIRMAELEKCLSKMGDDIPKKTRRAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFSLETEIAVLEQKIRAKVEQNQK 543
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A4S4DWI0 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 886.715 bits (2290), Expect = 0.000e+0
Identity = 436/554 (78.70%), Postives = 479/554 (86.46%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLGNASHNGV-----------VFCKPRKAVFP---RNSTSLRCEQ-QQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV SAFAG KLE + L N +               V CKP  A  P   R   ++RC+    +     ++I  N+     S+SLSAL+QLK SAADRYTKERSSIVVIGLS+HT PVEMREKLAIPEAEWPRAI ELC LNHIEEAAVLSTCNRMEIY VALSQHRGVKEVTEWMSKTSG+P  D+CEHRFLLYN DATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVRSE NIA+GAVSVSSA+VELALMKLP++SH TARML+IGAGKMGKLVIKHL AKGCT+MVVVNR+EERV AIREEL  ++IIYKPL++MLA AAEADVIFTSTASE PLFLKEHV DLPPVG +VG +RLF+DISVPRNVGSC+ +LETARVYNVDDLKEVV+ANKEDRLRKA EAQ II EESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MGDD++KKTK+A DDLSRGIVNK+LHGPMQHLRCDGS++RTL+ETLENMHALNRMFSLE E+SVLEQK+RAKVEQNQK
Sbjct:   19 MAVASAFAGAKLETLLLSNTAAVAASSPAVAASQIRVLCKPLGATRPLIHRARPTIRCQAASDVFLPTPDMIDPNTALASPSASLSALEQLKISAADRYTKERSSIVVIGLSVHTAPVEMREKLAIPEAEWPRAIEELCGLNHIEEAAVLSTCNRMEIYAVALSQHRGVKEVTEWMSKTSGIPIPDICEHRFLLYNKDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVTGFGRNISGLFKHAITVGKRVRSETNIAAGAVSVSSASVELALMKLPESSHKTARMLVIGAGKMGKLVIKHLVAKGCTQMVVVNRTEERVAAIREELKDVKIIYKPLSEMLACAAEADVIFTSTASEAPLFLKEHVMDLPPVGQEVGGLRLFIDISVPRNVGSCVTDLETARVYNVDDLKEVVAANKEDRLRKAMEAQAIIVEESKQFEAWRDSLETVPTIKKLRAYAERIRVAELEKCLSKMGDDISKKTKRAVDDLSRGIVNKILHGPMQHLRCDGSETRTLSETLENMHALNRMFSLETEMSVLEQKIRAKVEQNQK 572
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A0V0IMC1 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 884.404 bits (2284), Expect = 0.000e+0
Identity = 441/553 (79.75%), Postives = 490/553 (88.61%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLGNASHNGV---VFCKP--------RKAVFPRNSTSLRCEQQQLQTTNDNVIVDNS---TKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MA+P+AF+G KLE++    A+ +     +FC P        +K +F   ++ +RCE       +D  +VD S       SSSSLSAL+QLKSSAADRYTKERSSIVVIGLSIHTTPVE+REKLAIPEAEWPRAI ELC+LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVP +++C+HRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++ HSTARML+IGAGKMGKLVIKHL AKGCTKMVVVNRSE+RV+AIREE+  +EIIYKPL +ML  AAEADVIFTSTASETPLF+KEHV DLPPVG+ VGS+RLF+DISVPRNVG+C+ ELE ARVYNVDDLKEVV+ANKEDRLRKA EAQ II+EESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KC+S+MGDD++KKTKKA DDLSRGIVNKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMFSLE +ISVLEQK+RAKVEQ QK
Sbjct:    1 MAIPTAFSGAKLESLSSSAAAASPASIGLFCNPGRVRRLSIQKGLF---NSGIRCEV----AASD--VVDQSQSSGNVTSSSSLSALEQLKSSAADRYTKERSSIVVIGLSIHTTPVEVREKLAIPEAEWPRAIGELCNLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPVTEICKHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVTGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESCHSTARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEDRVSAIREEMKDVEIIYKPLNEMLKCAAEADVIFTSTASETPLFMKEHVVDLPPVGASVGSLRLFIDISVPRNVGACVNELEDARVYNVDDLKEVVAANKEDRLRKAMEAQAIISEESKQFEAWRDSLETVPTIKKLRAYAERIRVAELEKCMSKMGDDISKKTKKAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFSLETDISVLEQKIRAKVEQTQK 544
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5D2ZAV8 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 884.019 bits (2283), Expect = 0.000e+0
Identity = 436/568 (76.76%), Postives = 489/568 (86.09%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLG-------------NASHNGV-VFCKP---RKAVFPRNSTSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQKCASQGAVSTTLS 551
            MAV S F+G KLE + +              + SH  +  F KP   RKA+  R    +RCE  Q    N+   +D S     +S+LSAL+QLK+SAADRYTKERSSIVVIGLS+HT PVEMREKLAIPEAEWPRAI+ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+P S++CEHRFLLYN DATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQ VVGFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++SH+TARML+IGAGKMGKLVIKHL AKGCTKMVVVNRSEE+V AIREE+ G+EIIY+PLTDMLA +AEADV+FTSTASETPLFLKEHV DLPPV S+VG +RLFVDISVPRNVGSC+ ++E AR+YNVDDLKEVV+ANKEDRLRKA EAQ IIAEESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MG+D+ KKT++A DDLSRGIVNKLLHGPMQHLRCDGSD RTL+ETLENMHALNRMF LE++IS+ EQK+RAKVEQ+QK    G ++ + S
Sbjct:    1 MAVSSTFSGAKLERLLINSCSSPSASSLRACSLSHQQMKAFSKPNRGRKALAQRTG-GVRCEVAQSDAINEGEKLDPS----KASALSALEQLKTSAADRYTKERSSIVVIGLSVHTAPVEMREKLAIPEAEWPRAIAELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPVSEICEHRFLLYNKDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQSVVGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESSHATARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEEKVAAIREEMQGVEIIYRPLTDMLACSAEADVVFTSTASETPLFLKEHVKDLPPVSSEVGGLRLFVDISVPRNVGSCVSDVEGARLYNVDDLKEVVAANKEDRLRKAMEAQAIIAEESKQFEAWRDSLETVPTIKKLRAYAERIRVAELEKCLSKMGEDIPKKTRRAVDDLSRGIVNKLLHGPMQHLRCDGSDDRTLSETLENMHALNRMFGLESDISLFEQKIRAKVEQSQKIVEVGNLTISGS 563
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1S3XBH0 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 884.019 bits (2283), Expect = 0.000e+0
Identity = 432/548 (78.83%), Postives = 486/548 (88.69%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIF--------LGNASHNGVVFCKP-RKAVFPRNSTSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MA+P+AF+G KLE++         +G  SH G +   P +K +F   +  +RCE       + +    NS    SSSSLSAL+QLK+SAADRYTKERSSIVVIGLSIHTTPVE+REKLAIPEAEWPRAI ELC+LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVP +++C+HRFLLYNNDATQH+FEVSAGLDSLVLGEGQILAQVKQVVKVGQGV GFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++SH++ RML+IGAGKMGKLVIKHL AKGCT+MVVVNRSEERV+AIREE+  +EIIYKPL +ML ++AEADVIFTSTASETPLFLKEHV DLPPV + VG +RLFVDISVPRNVG+C+ ELE ARVYNVDDLKEVV+ANKEDRLRKA EAQ II+EESKQF AWRDSLETVPTIKKLRAYAER+R+AEL+KC+S+MGDD++KKT+KA DDLSRGIVNKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMF+LE +ISVLEQK+RAKVEQ QK
Sbjct:    1 MAIPTAFSGAKLESLSSSATSPAPIGLFSHPGRLRRLPIQKGLF---NLGIRCEVAASDVLSQS---QNSENVTSSSSLSALEQLKTSAADRYTKERSSIVVIGLSIHTTPVEIREKLAIPEAEWPRAIGELCNLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPVTEICKHRFLLYNNDATQHLFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVTGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESSHASTRMLVIGAGKMGKLVIKHLVAKGCTRMVVVNRSEERVSAIREEMKDVEIIYKPLGEMLNSSAEADVIFTSTASETPLFLKEHVLDLPPVAASVGGLRLFVDISVPRNVGACVNELENARVYNVDDLKEVVAANKEDRLRKAMEAQAIISEESKQFEAWRDSLETVPTIKKLRAYAERLRVAELEKCMSKMGDDISKKTRKAVDDLSRGIVNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFNLETDISVLEQKIRAKVEQTQK 542
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5D2Z9H6 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 883.634 bits (2282), Expect = 0.000e+0
Identity = 434/556 (78.06%), Postives = 484/556 (87.05%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFLG-------------NASHNGV-VFCKP---RKAVFPRNSTSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV S F+G KLE + +              + SH  +  F KP   RKA+  R    +RCE  Q    N+   +D S     +S+LSAL+QLK+SAADRYTKERSSIVVIGLS+HT PVEMREKLAIPEAEWPRAI+ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+P S++CEHRFLLYN DATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQ VVGFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++SH+TARML+IGAGKMGKLVIKHL AKGCTKMVVVNRSEE+V AIREE+ G+EIIY+PLTDMLA +AEADV+FTSTASETPLFLKEHV DLPPV S+VG +RLFVDISVPRNVGSC+ ++E AR+YNVDDLKEVV+ANKEDRLRKA EAQ IIAEESKQF AWRDSLETVPTIKKLRAYAERIR+AEL+KCLS+MG+D+ KKT++A DDLSRGIVNKLLHGPMQHLRCDGSD RTL+ETLENMHALNRMF LE++IS+ EQK+RAKVEQ+QK
Sbjct:    1 MAVSSTFSGAKLERLLINSCSSPSASSLRACSLSHQQMKAFSKPNRGRKALAQRTG-GVRCEVAQSDAINEGEKLDPS----KASALSALEQLKTSAADRYTKERSSIVVIGLSVHTAPVEMREKLAIPEAEWPRAIAELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPVSEICEHRFLLYNKDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQSVVGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESSHATARMLVIGAGKMGKLVIKHLVAKGCTKMVVVNRSEEKVAAIREEMQGVEIIYRPLTDMLACSAEADVVFTSTASETPLFLKEHVKDLPPVSSEVGGLRLFVDISVPRNVGSCVSDVEGARLYNVDDLKEVVAANKEDRLRKAMEAQAIIAEESKQFEAWRDSLETVPTIKKLRAYAERIRVAELEKCLSKMGEDIPKKTRRAVDDLSRGIVNKLLHGPMQHLRCDGSDDRTLSETLENMHALNRMFGLESDISLFEQKIRAKVEQSQK 551
[Close]
BLAST of DCAR_009549 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7J6H526 (Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584} (1.2.1.70 {ECO:0000256|ARBA:ARBA00012970, ECO:0000256|RuleBase:RU000584}))

HSP 1 Score: 883.248 bits (2281), Expect = 0.000e+0
Identity = 433/556 (77.88%), Postives = 481/556 (86.51%), Query Frame = 0
 
Query:    1 MAVPSAFAGPKLENIFL--------------GNASHNGVVFCKP---RKAVFPRNSTSLRCEQQQLQTTNDNVIVDNSTKTPSSSSLSALQQLKSSAADRYTKERSSIVVIGLSIHTTPVEMREKLAIPEAEWPRAISELCSLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGVPASDLCEHRFLLYNNDATQHIFEVSAGLDSLVLGEGQILAQVKQVVKVGQGVVGFGRNISGLFKHAITVGKRVRSELNIASGAVSVSSAAVELALMKLPKTSHSTARMLLIGAGKMGKLVIKHLAAKGCTKMVVVNRSEERVTAIREELHGIEIIYKPLTDMLAAAAEADVIFTSTASETPLFLKEHVADLPPVGSDVGSVRLFVDISVPRNVGSCIKELETARVYNVDDLKEVVSANKEDRLRKAKEAQTIIAEESKQFAAWRDSLETVPTIKKLRAYAERIRLAELDKCLSRMGDDVTKKTKKAADDLSRGIVNKLLHGPMQHLRCDGSDSRTLTETLENMHALNRMFSLEAEISVLEQKVRAKVEQNQK 539
            MAV ++FAG KLE +                  +S     FCKP   R+A+  R    +RC+    +T+         T  P  S++SAL+QLK+SAADRYTKERSSIVVIGLS+HTTPVE+REKLAIPEAEWPRAI ELC LNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSG+PAS++C+HRFLLYN DATQH+FEVSAGLDSLVLGEGQILAQVKQVVKVGQG+VGFGRNISGLFKHAITVGKRVR+E NIA+GAVSVSSAAVELALMKLP++SH+TARML+IGAGKMGKLVIKHL AKGCTKM+VVNRSEERV AIREE++G+EIIYKPLT+ML  AAEADV+FTSTASETPLFLKEHV DLP V  + G  RLFVDISVPRNVGSC+ E+ETAR+YNVDDLKEVV+ANKEDRLRKA EAQ IIA+ESKQF AWRDSLETVPTIKKLRAYAERIR AEL+KCLS+MGDD++KKT+KA DDLSRGI+NKLLHGPMQHLRCDGSDSRTL+ETLENMHALNRMFSLE EISVLEQK+RAKVEQ QK
Sbjct:    1 MAVSTSFAGAKLEALLFKSSSANTTTSTSRVAPSSSPLSSFCKPIRARRALIQRGV--VRCDVSASETSVQ-------TNEPGGSNISALEQLKTSAADRYTKERSSIVVIGLSVHTTPVEIREKLAIPEAEWPRAIGELCGLNHIEEAAVLSTCNRMEIYVVALSQHRGVKEVTEWMSKTSGIPASEICKHRFLLYNKDATQHLFEVSAGLDSLVLGEGQILAQVKQVVKVGQGIVGFGRNISGLFKHAITVGKRVRTETNIAAGAVSVSSAAVELALMKLPESSHTTARMLVIGAGKMGKLVIKHLVAKGCTKMMVVNRSEERVAAIREEINGVEIIYKPLTEMLTCAAEADVVFTSTASETPLFLKEHVKDLPAVDQETGGYRLFVDISVPRNVGSCVGEVETARIYNVDDLKEVVAANKEDRLRKAMEAQAIIADESKQFEAWRDSLETVPTIKKLRAYAERIRAAELEKCLSKMGDDISKKTRKAVDDLSRGIMNKLLHGPMQHLRCDGSDSRTLSETLENMHALNRMFSLETEISVLEQKIRAKVEQTQK 547
Match NameStatsDescription
A0A7J7HRD1E-Value: 0.000e+0, PID: 79.53Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A6J1K420E-Value: 0.000e+0, PID: 79.89Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A6J1BVE9E-Value: 0.000e+0, PID: 78.48Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A6J1HDK8E-Value: 0.000e+0, PID: 79.71Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A4S4DWI0E-Value: 0.000e+0, PID: 78.70Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A0V0IMC1E-Value: 0.000e+0, PID: 79.75Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A5D2ZAV8E-Value: 0.000e+0, PID: 76.76Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A1S3XBH0E-Value: 0.000e+0, PID: 78.83Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A5D2Z9H6E-Value: 0.000e+0, PID: 78.06Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]
A0A7J6H526E-Value: 0.000e+0, PID: 77.88Glutamyl-tRNA reductase {ECO:0000256|ARBA:ARBA0001... [more]

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Analysis: 
NameDescription
Carrot Genome Assembly DCARv2

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
DCAR peptide blastp to SwissProt and TrEMBL without DCAR

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.
DCAR V1.0 Gene Prediction

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.