DCAR_029713

Resource Type: 
Polypeptide
Name: 
DCAR_029713
Identifier: 
DCAR_029713.mRNA-protein
Sequence: 
MLLFVNVPWQFCTGEYRKAGLPVGYKNCQFHRGDGSGCVSIYGSKFDDEN
FIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGL
LVVRKIENVATGQQNRPKLPCIIAECGEM*
Sequence Length: 
130
Sequence Checksum: 
8562261d92cac3385d1f66391c6e38d2
View location in JBrowse: 
DCARv2_Chr9:12187872..12192876+
Organism: 
Daucus carota subspecies sativus
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, DCAR_029713, derives from mRNA, DCAR_029713.
Blast Results: 
The following BLAST results are available for this feature:
BLAST of DCAR_029713 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_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6S7LL24 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 231.106 bits (588), Expect = 2.299e-76
Identity = 113/134 (84.33%), Postives = 117/134 (87.31%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRK+GLPVGYK CQFHR              GDGSGCVSIYGSKF+DENFIAKHTGPGLLSMANSGPN+NGCQFF+TCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKLPCIIAECGEM
Sbjct:   60 QFCTGEYRKSGLPVGYKGCQFHRIIKDFMIQAGDFLKGDGSGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNSNGCQFFLTCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLPCIIAECGEM 193
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7J7GPE4 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 229.95 bits (585), Expect = 6.515e-76
Identity = 114/134 (85.07%), Postives = 115/134 (85.82%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYGSKF+DENFIAKHTGPGLLSMANSGPN NGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKL CIIAECGEM
Sbjct:   66 QFCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACIIAECGEM 199
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6I9U4W6 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 229.565 bits (584), Expect = 7.507e-76
Identity = 112/134 (83.58%), Postives = 116/134 (86.57%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYGSKFDDENF+AKHTGPGLLSMANSGPN+NGCQFFITCAKCDWLDNKHVVFGRVLGDGLL+VRKIENVATG  NRPKL C+IAECGEM
Sbjct:   61 QFCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGSKFDDENFVAKHTGPGLLSMANSGPNSNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLIVRKIENVATGPNNRPKLACVIAECGEM 194
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A251TBA2 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 229.565 bits (584), Expect = 7.836e-76
Identity = 113/134 (84.33%), Postives = 116/134 (86.57%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGE+RKAGLPVGYK CQFHR              GDGSGCVSIYGSKF+DENFIAKHTGPGLLSMANSGPN NGCQFFITCAKCDWLDNKHVVFGRVLGDGLLV+RKIENVATG  NRPKLPCIIAECGEM
Sbjct:   56 QFCTGEFRKAGLPVGYKGCQFHRIIKDFMIQAGDFLKGDGSGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVMRKIENVATGPNNRPKLPCIIAECGEM 189
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: U5GNT9 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 228.794 bits (582), Expect = 1.562e-75
Identity = 112/134 (83.58%), Postives = 115/134 (85.82%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYG KF+DENF+AKHTGPGLLSMANSGPN NGCQFF+TCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKLPCIIAECGEM
Sbjct:   54 QFCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGLKFEDENFVAKHTGPGLLSMANSGPNTNGCQFFMTCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLPCIIAECGEM 187
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2R6QKH4 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 228.409 bits (581), Expect = 1.946e-75
Identity = 112/134 (83.58%), Postives = 115/134 (85.82%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYGSKF+DENFIAKHTGPGLLSMANSGPN NGCQFF+TCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKL C+IAECGEM
Sbjct:   58 QFCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQFFLTCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACVIAECGEM 191
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6P4AZB7 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 228.409 bits (581), Expect = 2.011e-75
Identity = 113/134 (84.33%), Postives = 114/134 (85.07%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYG KFDDENFIAKHTGPGLLSMANSGPN NGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKL C+IAECGEM
Sbjct:   58 QFCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGHKFDDENFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACVIAECGEM 191
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: B9GX77 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 228.024 bits (580), Expect = 3.256e-75
Identity = 111/134 (82.84%), Postives = 115/134 (85.82%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            QFCTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYG KF+DENF+AKHTGPGLLSMANSGPN NGCQFFITCAKCDWLDNKHVVFGRVLGDGLLV+RKIENVATG  NRPKLPC+IAECGEM
Sbjct:   56 QFCTGEYRKAGLPVGYKVCQFHRVIKDFMIQAGDFLKGDGSGCVSIYGLKFEDENFVAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVIRKIENVATGPNNRPKLPCVIAECGEM 189
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A7G5F3P2 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 228.024 bits (580), Expect = 3.440e-75
Identity = 112/134 (83.58%), Postives = 113/134 (84.33%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            Q CTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYG KFDDENF AKHTGPGLLSMANSGPN NGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKLPC+IAECGEM
Sbjct:   57 QLCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFVKGDGSGCVSIYGHKFDDENFTAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLPCVIAECGEM 190
[Close]
BLAST of DCAR_029713 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5J5B675 (Peptidyl-prolyl cis-trans isomerase {ECO:0000256|RuleBase:RU363019} (PPIase {ECO:0000256|RuleBase:RU363019}) (5.2.1.8 {ECO:0000256|RuleBase:RU363019}))

HSP 1 Score: 227.639 bits (579), Expect = 3.473e-75
Identity = 112/134 (83.58%), Postives = 115/134 (85.82%), Query Frame = 0
 
Query:   10 QFCTGEYRKAGLPVGYKNCQFHR--------------GDGSGCVSIYGSKFDDENFIAKHTGPGLLSMANSGPNANGCQFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGQQNRPKLPCIIAECGEM 129
            Q CTGEYRKAGLPVGYK CQFHR              GDGSGCVSIYGSKF+DENFIAKHTGPGLLSMANSGPN+NGCQFF+TCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATG  NRPKL CIIAECGEM
Sbjct:   50 QLCTGEYRKAGLPVGYKGCQFHRVIKDFMIQAGDFVKGDGSGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNSNGCQFFMTCAKCDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACIIAECGEM 183
Match NameStatsDescription
A0A6S7LL24E-Value: 2.299e-76, PID: 84.33Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A7J7GPE4E-Value: 6.515e-76, PID: 85.07Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A6I9U4W6E-Value: 7.507e-76, PID: 83.58Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A251TBA2E-Value: 7.836e-76, PID: 84.33Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
U5GNT9E-Value: 1.562e-75, PID: 83.58Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A2R6QKH4E-Value: 1.946e-75, PID: 83.58Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A6P4AZB7E-Value: 2.011e-75, PID: 84.33Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
B9GX77E-Value: 3.256e-75, PID: 82.84Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A7G5F3P2E-Value: 3.440e-75, PID: 83.58Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]
A0A5J5B675E-Value: 3.473e-75, PID: 83.58Peptidyl-prolyl cis-trans isomerase {ECO:0000256|R... [more]

Pages

back to top
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.