DCAR_002339

Resource Type: 
Polypeptide
Name: 
DCAR_002339
Identifier: 
DCAR_002339.mRNA-protein
Sequence: 
MAAVVKGGTRPPWVGLGAAVWVQIAAGNAYTFPLYSHSLKSVLGFTQQQL
TILGVANDIGENVGILPGIASNKFPPWVVMFVGVFAAFFGYGVIWLAVSQ
TVPSMPYWVLWVALVIATNSSAWFGTAVLVTNMRNFPLSRGTVAGILKGY
VGLSAAVYTEVHSMLLGGSAENLLLFMTIGIPVTCLAMMYFVRACTPALG
EDSSEHVHFLFTQVSSLALAVYLLTTTILKSIVPISRSISYTLIGIMVVL
LMSPLAIPIKMTLFPASSKKIGKQASSSDDIVTEDGESDLTGPLLSSFSS
DINLLGLYENEDVSEVDILLAMGEGAIKKKRKPRRGEDFKFREAVIKADF
WLLWVVYFLGVGSGVTVLNNLAEIGVSLGVNDTTILLSLFSFCNFLGRLG
AGVVSEHFVRSKAIPRTLWMTVTQVLMIIIYLLYASALHGTLYAATALLG
ICFGVQFGIMIPTVSELFGLKDFGIIFNFMQLGNPIGALLFSGLVAGYVY
DSEAAKQLSSSCLGPTCFRLTFLFLAGVCGLGTILSIVLTIRIRPVYQML
YAGGSFRLPNGASS*
Sequence Length: 
565
Sequence Checksum: 
ee0f7a6a5f0a56843217790f4c246424
View location in JBrowse: 
DCARv2_Chr1:28443383..28446497-
Organism: 
Daucus carota subspecies sativus
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, DCAR_002339, derives from mRNA, DCAR_002339.
Blast Results: 
The following BLAST results are available for this feature:
BLAST of DCAR_002339 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
Position :
0
Zoom :
x 1
50100150200250300350400450500550Expect = 0.00e+0, Id = 79.32Expect = 0.00e+0, Id = 77.54Expect = 0.00e+0, Id = 77.18Expect = 0.00e+0, Id = 77.36Expect = 0.00e+0, Id = 77.36Expect = 0.00e+0, Id = 77.58Expect = 0.00e+0, Id = 76.83Expect = 0.00e+0, Id = 76.65Expect = 0.00e+0, Id = 76.83Expect = 0.00e+0, Id = 76.65SequenceA0A5B7C915A0A0V0IKS4M1B3Z3A0A1U7Y252A0A1S4DP21A0A5J5BH97A0A6N2BC12A0A2G3CZG6A0A1U8G2M2A0A2G3A2R1
Match NameStatsDescription
A0A5B7C915E-Value: 0.000e+0, PID: 79.32Nodulin-like domain-containing protein {ECO:000025... [more]
A0A0V0IKS4E-Value: 0.000e+0, PID: 77.54(Putative transporter mch1-like {ECO:0000313|EMBL:... [more]
M1B3Z3E-Value: 0.000e+0, PID: 77.18(Nodulin {ECO:0000313|EnsemblPlants:PGSC0003DMT400... [more]
A0A1U7Y252E-Value: 0.000e+0, PID: 77.36(uncharacterized protein LOC104244484 {ECO:0000313... [more]
A0A1S4DP21E-Value: 0.000e+0, PID: 77.36(protein NUCLEAR FUSION DEFECTIVE 4-like {ECO:0000... [more]
A0A5J5BH97E-Value: 0.000e+0, PID: 77.58Nodulin-like domain-containing protein {ECO:000025... [more]
A0A6N2BC12E-Value: 0.000e+0, PID: 76.83Nodulin-like domain-containing protein {ECO:000025... [more]
A0A2G3CZG6E-Value: 0.000e+0, PID: 76.65Nodulin-like domain-containing protein {ECO:000025... [more]
A0A1U8G2M2E-Value: 0.000e+0, PID: 76.83(protein NUCLEAR FUSION DEFECTIVE 4 isoform X1 {EC... [more]
A0A2G3A2R1E-Value: 0.000e+0, PID: 76.65Nodulin-like domain-containing protein {ECO:000025... [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.