MAAEDGGVIVDGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIP
SPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQR
SGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQE
YVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNV
PSQPMEIPPPSRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVV
YKSTQR*
| Relationships |
|---|
| The polypeptide, DCAR_030836, derives from mRNA, DCAR_030836. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A5B7C670 (AMPKBI domain-containing protein {ECO:0000259|SMART:SM01010})
HSP 1 Score: 427.557 bits (1098), Expect = 1.966e-150
Identity = 211/270 (78.15%), Postives = 225/270 (83.33%), Query Frame = 0
Query: 2 AAEDGGV---------------IVDGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPPSRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
AEDGGV DGE MG SPP +PRAA SPLMFTPQ PVVPLQRPDEMHIPS SWMQTTS YEDI SEQGIPTMITWSYD EV VEGSWD+WKTRKPLQRSGKDFTI+KVLPSGVY+YRFIVDGQWRYAPD+P QDDAGNA NILDLQ+YVPEDI+SI+GF PPQSP+SSYNN QLG ED+AKEPP+VPPHLQMTLLNVPS +PP SRPQHVVLNHLYMQKGR +VVALGSTHRF SKYVTVV+YKS QR
Sbjct: 19 GAEDGGVGGALDDMAPLDAAHGDGDGELMGQSPPPTPRAAHSPLMFTPQVPVVPLQRPDEMHIPSHSWMQTTSGYEDICSEQGIPTMITWSYDGKEVSVEGSWDNWKTRKPLQRSGKDFTIMKVLPSGVYQYRFIVDGQWRYAPDMPCAQDDAGNACNILDLQDYVPEDIKSISGFEPPQSPESSYNNLQLGCEDYAKEPPLVPPHLQMTLLNVPSSTEILPPFSRPQHVVLNHLYMQKGRGGPSVVALGSTHRFLSKYVTVVLYKSLQR 288
Match: A0A5J5B3U7 (AMPKBI domain-containing protein {ECO:0000259|SMART:SM01010})
HSP 1 Score: 427.557 bits (1098), Expect = 1.977e-150
Identity = 205/247 (83.00%), Postives = 221/247 (89.47%), Query Frame = 0
Query: 11 DGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
D E MG SPP SPRAA SPLMFTPQ PVVPLQRP EMHIPS SWMQTTS YED+ EQGIPTMITWSY+ EVFVEGSWD+WKTRKPLQ+SGKDFTI+KVLPSGVY+YRFIVDGQWRYAPD+PW QDDAGN NILDLQ+YVPED+ESI+GF PPQSP+SSYNN QLG+ED+AKEPP+VPPHLQMTLLNVPS MEIPPP SRPQHVVLNHLYMQKGR +VVALGSTHRF SKYVTVV+YKS QR
Sbjct: 44 DAELMGQSPPPSPRAAHSPLMFTPQVPVVPLQRPGEMHIPSHSWMQTTSEYEDMCCEQGIPTMITWSYEGKEVFVEGSWDNWKTRKPLQKSGKDFTIMKVLPSGVYQYRFIVDGQWRYAPDMPWAQDDAGNTCNILDLQDYVPEDVESISGFEPPQSPESSYNNLQLGSEDYAKEPPLVPPHLQMTLLNVPSSYMEIPPPHSRPQHVVLNHLYMQKGRGGPSVVALGSTHRFLSKYVTVVLYKSLQR 290
Match: A0A834X8S1 ((SNF1-related protein kinase regulatory subunit beta-2 {ECO:0000313|EMBL:KAF7840516.1}))
HSP 1 Score: 422.935 bits (1086), Expect = 1.145e-148
Identity = 202/248 (81.45%), Postives = 222/248 (89.52%), Query Frame = 0
Query: 10 VDGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
V E MG SPP+SPRA QSPLMFTPQ PVVPLQRPDEM PS SWMQ +SAYED+ SEQGIPTMITWSYD EV VEGSWD+WKTR PLQRSGKDFTI+KVLPSGVY+YRF+VDGQWRYA DLPW QDDAGNAYNILDLQ+YVPEDI SI+GF PPQSPDSSY+N QLG+ED+AKEPP+VPPHLQMTLLN+P+ MEIPPP SRPQHVVLNHLYMQKG+SS +VVALG+THRF +KYVTVV+YKS QR
Sbjct: 37 VSSELMGQSPPTSPRATQSPLMFTPQVPVVPLQRPDEMQAPSHSWMQASSAYEDMCSEQGIPTMITWSYDGKEVAVEGSWDNWKTRMPLQRSGKDFTIMKVLPSGVYQYRFLVDGQWRYALDLPWAQDDAGNAYNILDLQDYVPEDIGSISGFEPPQSPDSSYSNLQLGSEDYAKEPPLVPPHLQMTLLNIPATNMEIPPPLSRPQHVVLNHLYMQKGKSSPSVVALGTTHRFLAKYVTVVLYKSLQR 284
Match: A0A2R6QM04 ((SNF1-related protein kinase regulatory subunit beta-2 like {ECO:0000313|EMBL:PSS10440.1}))
HSP 1 Score: 422.55 bits (1085), Expect = 1.718e-148
Identity = 201/245 (82.04%), Postives = 222/245 (90.61%), Query Frame = 0
Query: 13 EFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
+ MG SPPSSPRAAQSPLMFTPQ PV+PLQRPDE+H PS SWM+T + YEDI SEQGIPTMITWSYD EV VEGSWD+WK+RKPLQRSGKDFT++KVLPSGVY+YRFIVDGQWRYAPD+PW QDD GNAYNILDLQ+YVPED+ESI+GF PQSP+SSYNN QLG+ED+AKEPP+VPPHLQ TLLNVPS MEIPPP SRPQHVVLNHLYMQKGRSS +VVALGSTHRF +KYVTVV+YKS QR
Sbjct: 44 DLMGHSPPSSPRAAQSPLMFTPQVPVLPLQRPDEIHAPSHSWMETATGYEDICSEQGIPTMITWSYDGTEVSVEGSWDNWKSRKPLQRSGKDFTLMKVLPSGVYQYRFIVDGQWRYAPDMPWAQDDTGNAYNILDLQDYVPEDVESISGFESPQSPESSYNNLQLGSEDYAKEPPLVPPHLQTTLLNVPSSYMEIPPPLSRPQHVVLNHLYMQKGRSSPSVVALGSTHRFLAKYVTVVLYKSIQR 288
Match: A0A2R6RB24 ((SNF1-related protein kinase regulatory subunit beta-2 like {ECO:0000313|EMBL:PSS24757.1}))
HSP 1 Score: 418.698 bits (1075), Expect = 5.086e-147
Identity = 200/245 (81.63%), Postives = 221/245 (90.20%), Query Frame = 0
Query: 13 EFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
+ MG SPPSSPRAAQSPLMFTPQ PV+PLQRPDEM+ PS SWMQT + YEDI SEQGIPTMITWSYD EV VEGSWD+WKTRKPLQRSGKDFT++KVLPSGVY+Y+FIVDGQWRY PD+PW QDD GNAYNILDLQ+YVPED+ESI+GF PPQSP+SSY N QLG+ED+AKEPP+VPPHLQMTLL VPS MEIPPP SRPQHVVLNHLY+QKGRSS +VVALGSTHRF +KYVTVV+YKS QR
Sbjct: 41 DLMGHSPPSSPRAAQSPLMFTPQVPVLPLQRPDEMNAPSHSWMQTATGYEDICSEQGIPTMITWSYDGKEVSVEGSWDNWKTRKPLQRSGKDFTLMKVLPSGVYQYKFIVDGQWRYTPDMPWAQDDTGNAYNILDLQDYVPEDVESISGFEPPQSPESSYTNLQLGSEDYAKEPPLVPPHLQMTLLKVPSSYMEIPPPLSRPQHVVLNHLYIQKGRSSPSVVALGSTHRFVAKYVTVVLYKSIQR 285
Match: A0A2J6K5H9 (AMPKBI domain-containing protein {ECO:0000259|SMART:SM01010})
HSP 1 Score: 416.001 bits (1068), Expect = 6.694e-146
Identity = 204/261 (78.16%), Postives = 225/261 (86.21%), Query Frame = 0
Query: 1 MAAEDGGVIV----DGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
+AA+D I DGEFMG SPP SPR + SPLMFTPQ PV PLQRPDEM P+ SWM T+S+YED+ SEQGIPTMITWSYD EV VEGSWD+WKTRK LQRSGKDF ILKVLPSGVY+YRF+VDGQWRY+PD+PWTQD+AGN YNILDLQEYVPEDI+SI+GF PPQSPDSSYNN QLG ED+AKEPP+VPPHLQMTLLN PS MEIPPP SRPQHVV+NHLYMQKGRSS +VVALGSTHRF SKYVTVV+YKS +
Sbjct: 27 VAAQDANYIARTGDDGEFMGHSPPPSPRVSGSPLMFTPQVPVAPLQRPDEMQ-PNNSWMHTSSSYEDMMSEQGIPTMITWSYDGKEVAVEGSWDNWKTRKALQRSGKDFIILKVLPSGVYQYRFVVDGQWRYSPDVPWTQDEAGNTYNILDLQEYVPEDIQSISGFDPPQSPDSSYNNLQLGCEDYAKEPPLVPPHLQMTLLNAPSPHMEIPPPSSRPQHVVINHLYMQKGRSSDSVVALGSTHRFLSKYVTVVLYKSIHQ 286
Match: A0A6S7N222 (AMPKBI domain-containing protein {ECO:0000259|SMART:SM01010})
HSP 1 Score: 416.001 bits (1068), Expect = 6.694e-146
Identity = 204/261 (78.16%), Postives = 225/261 (86.21%), Query Frame = 0
Query: 1 MAAEDGGVIV----DGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
+AA+D I DGEFMG SPP SPR + SPLMFTPQ PV PLQRPDEM P+ SWM T+S+YED+ SEQGIPTMITWSYD EV VEGSWD+WKTRK LQRSGKDF ILKVLPSGVY+YRF+VDGQWRY+PD+PWTQD+AGN YNILDLQEYVPEDI+SI+GF PPQSPDSSYNN QLG ED+AKEPP+VPPHLQMTLLN PS MEIPPP SRPQHVV+NHLYMQKGRSS +VVALGSTHRF SKYVTVV+YKS +
Sbjct: 27 VAAQDANYIARTGDDGEFMGHSPPPSPRVSGSPLMFTPQVPVAPLQRPDEMQ-PNNSWMHTSSSYEDMMSEQGIPTMITWSYDGKEVAVEGSWDNWKTRKALQRSGKDFIILKVLPSGVYQYRFVVDGQWRYSPDVPWTQDEAGNTYNILDLQEYVPEDIQSISGFDPPQSPDSSYNNLQLGCEDYAKEPPLVPPHLQMTLLNAPSPHMEIPPPSSRPQHVVINHLYMQKGRSSDSVVALGSTHRFLSKYVTVVLYKSIHQ 286
Match: A0A1U7W8U5 ((SNF1-related protein kinase regulatory subunit beta-2 {ECO:0000313|RefSeq:XP_009773626.1}))
HSP 1 Score: 411.764 bits (1057), Expect = 2.614e-144
Identity = 195/249 (78.31%), Postives = 225/249 (90.36%), Query Frame = 0
Query: 9 IVDGEFM-GPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPPSRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
I+DGE + G SPPSSPRA+QSPLMF PQ PVVPLQRP+E+HIP+PSWMQTTS Y+D++ EQG+PT+I+W++D EV VEGSWD+WK+R PLQRSGKDFTILKVLPSGVY+YRFIVDGQWR +PDLP QD+ GN YNILD+++YVPEDIESI+GF PPQSPDSSY+N QLGAED+AKEPP+VPPHLQMTLLNVPS MEIPP SRPQHVVLNHLYMQKGRS+ +VVALGST+RF SKYVTVV+YKS QR
Sbjct: 36 IMDGELIAGHSPPSSPRASQSPLMFRPQMPVVPLQRPEEVHIPNPSWMQTTSGYDDLNDEQGVPTLISWTHDGKEVSVEGSWDNWKSRNPLQRSGKDFTILKVLPSGVYQYRFIVDGQWRCSPDLPCVQDEVGNTYNILDVKDYVPEDIESISGFEPPQSPDSSYSNLQLGAEDYAKEPPLVPPHLQMTLLNVPSSHMEIPPLSRPQHVVLNHLYMQKGRSTPSVVALGSTNRFLSKYVTVVLYKSIQR 284
Match: A0A2G2VD87 ((SNF1-related protein kinase regulatory subunit beta-2 {ECO:0000313|EMBL:PHT30899.1}))
HSP 1 Score: 411.379 bits (1056), Expect = 4.029e-144
Identity = 195/247 (78.95%), Postives = 221/247 (89.47%), Query Frame = 0
Query: 11 DGEFMGPSPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
DGE MG SPPSSPRA+ SP MF PQ PVVPLQRP+E+HIP+PSWMQTTS YED++ EQG+PT+I+W+YD EV VEGSWD+WK+R PLQRSGKDFTILKVLPSGVY+YRFIVDGQWR +PDLP QD+AGN YNILD+++YVPEDIESI+ F PP SPDSSY+N QLGAED+AKEPP+VPPHLQMTLLNVPS ME+PPP SRPQHVVLNHLYMQKGRSS +VVALGST+RF SKYVTVV+YKS QR
Sbjct: 36 DGELMGQSPPSSPRASHSPFMFRPQIPVVPLQRPEELHIPNPSWMQTTSGYEDLNDEQGVPTLISWTYDGKEVAVEGSWDNWKSRNPLQRSGKDFTILKVLPSGVYQYRFIVDGQWRCSPDLPCIQDEAGNTYNILDVKDYVPEDIESISCFEPPLSPDSSYSNMQLGAEDYAKEPPLVPPHLQMTLLNVPSSHMEVPPPLSRPQHVVLNHLYMQKGRSSPSVVALGSTNRFLSKYVTVVLYKSIQR 282
Match: A0A1S4DRL1 ((SNF1-related protein kinase regulatory subunit beta-2-like {ECO:0000313|RefSeq:XP_016516065.1}))
HSP 1 Score: 410.609 bits (1054), Expect = 8.372e-144
Identity = 196/250 (78.40%), Postives = 226/250 (90.40%), Query Frame = 0
Query: 9 IVDGEFMGP-SPPSSPRAAQSPLMFTPQAPVVPLQRPDEMHIPSPSWMQTTSAYEDISSEQGIPTMITWSYDANEVFVEGSWDDWKTRKPLQRSGKDFTILKVLPSGVYRYRFIVDGQWRYAPDLPWTQDDAGNAYNILDLQEYVPEDIESIAGFGPPQSPDSSYNNSQLGAEDFAKEPPIVPPHLQMTLLNVPSQPMEIPPP-SRPQHVVLNHLYMQKGRSSSAVVALGSTHRFFSKYVTVVVYKSTQR 256
I+DGE +G SPPSSPRA+QSPLMF PQ PVVPLQRP+E+HIP+PSWMQTTS Y+D++ EQG+PT+I+W++D EV VEGSWD+WK+R PLQRSGKDFTILKVLPSGVY+YRFIVDGQWR +PDLP QD+ GN YNILD+++YVPEDIESI+GF PPQSPDSSY+N QLGAED+AKEPP+VPPHLQMTLLNVPS MEIPPP SRPQHVVLNHLYMQKGRS+ +VVALGST+RF SKYVTVV+YKS QR
Sbjct: 32 IMDGELIGAHSPPSSPRASQSPLMFRPQMPVVPLQRPEEVHIPNPSWMQTTSGYDDLNDEQGVPTLISWTHDGKEVAVEGSWDNWKSRNPLQRSGKDFTILKVLPSGVYQYRFIVDGQWRCSPDLPSVQDEVGNTYNILDVKDYVPEDIESISGFEPPQSPDSSYSNLQLGAEDYAKEPPLVPPHLQMTLLNVPSSHMEIPPPLSRPQHVVLNHLYMQKGRSTPSVVALGSTNRFLSKYVTVVLYKSIQR 281
| Match Name | Stats | Description |
|---|---|---|
| A0A5B7C670 | E-Value: 1.966e-150, PID: 78.15 | AMPKBI domain-containing protein {ECO:0000259|SMAR... [more] |
| A0A5J5B3U7 | E-Value: 1.977e-150, PID: 83.00 | AMPKBI domain-containing protein {ECO:0000259|SMAR... [more] |
| A0A834X8S1 | E-Value: 1.145e-148, PID: 81.45 | (SNF1-related protein kinase regulatory subunit be... [more] |
| A0A2R6QM04 | E-Value: 1.718e-148, PID: 82.04 | (SNF1-related protein kinase regulatory subunit be... [more] |
| A0A2R6RB24 | E-Value: 5.086e-147, PID: 81.63 | (SNF1-related protein kinase regulatory subunit be... [more] |
| A0A2J6K5H9 | E-Value: 6.694e-146, PID: 78.16 | AMPKBI domain-containing protein {ECO:0000259|SMAR... [more] |
| A0A6S7N222 | E-Value: 6.694e-146, PID: 78.16 | AMPKBI domain-containing protein {ECO:0000259|SMAR... [more] |
| A0A1U7W8U5 | E-Value: 2.614e-144, PID: 78.31 | (SNF1-related protein kinase regulatory subunit be... [more] |
| A0A2G2VD87 | E-Value: 4.029e-144, PID: 78.95 | (SNF1-related protein kinase regulatory subunit be... [more] |
| A0A1S4DRL1 | E-Value: 8.372e-144, PID: 78.40 | (SNF1-related protein kinase regulatory subunit be... [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. |