LOC108220639

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108220639
Identifier: 
LOC108220639
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017394451.1, is a part of gene, LOC108220639.
The genetic_marker, MK002866 K0310, is located in gene, LOC108220639.
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
NCBI Daucus carota subsp. sativus Annotation Release 100

The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/

Data from this analysis can be viewed in JBrowse here.
Transcripts: 
Transcript NameIdentifierTypeLocation
XM_017394451.1XM_017394451.1mRNADCARv2_Chr5:34173680..34181356
Sequence: 
ACAAAAGGCAATTAATAACTGCAAATCTCCATCGAGGGGAGGGAAGTCTC
TGAATAATTCCGGCCATCATCATCAATTCATCATCTATTCATCTCGTCGT
CATTAATAACAAACTCCAATTATATAAACAATTTTAAAAGAAAAGGATAA
ACAACGACAGATACATAACCATATATCTTTGAGTTCGTTTGCACATATAC
ACAATTGAAATCGGTGCCTTGGTGGTGAAGTTGAAGGGAATTAGGGTTAA
TCAAATGCTCTTTGTCTGTCATCGATCATCGTCATCAGGATGCCACCGCA
TACATTGACGCCTCGCAGCTCCGCTTATCTCACCGCTCTTACTCAGGAGA
TCGAGAAAAAACTTCAACGAGTCTCTCTCTCTCTCTCTCTCCCTCCCTCC
CCCCCTCCCTCCCTCTATATATGTAGATTGATGTTGCGAGGGATTGCTTT
TTCTTTCATAATTCATGTTTGTGTATATATGTGTTGAGATAATTGAGTTT
CGGATTGACAGGGAATAGCTTCCCCGACGCTGAGTCGCAATTTACTGCAA
GAACTCTTTCAGGACATTGCTTTAGAAGTTGATGATCGTGCTAAAGGTTG
ATTTAATTCTGTCATGTCCTTTGGTTTCGATGCTTCTTTCAAACATTGTT
ACTCTCTGTGTTTGGATTTTATTTACCGTATGTTACTGTTTTAGTAAATA
GTGCTAGCGTATTTAGGCATTTTTCAGGAATTGCTCCAAACTGTTCCCTA
AAACGACTCTTTATTATCCATCTTAACTGTGTAAAAAAAAACTATATACT
GTTTGCTACAAGACATTTGTTTCATTTAAGTACTTATCGTTGTTTGAGTA
TGACAGTACTAATCAGCAAGCTAGATGTGTTAATATATCAGGATAATTTA
GAAAATGTTTTTGAAACAGTAACTGGTTTTTATAACTTTTGTCGTGATGT
TTTCGCGAATCAGAGAATTAAATTTATTAGTGAACAAAACGACACAATGT
TGTGATTCTCAGTCTGTCCTTGGATGGAACATTTATTTTTATATTTTTTA
TATGTTTTGTCGGGATTGTGTAAAAGAAGCATGTTGTAACGTCTTCTGAC
CTATAGTTTTGGCTGCTTTATTGGTGATTAAATGTTTTGAGTAGTGAAAT
GTGCTTGTACTGACCTGGAGAAGTCACATATACAGATATCAATTGTGTGC
ATTATGCATCATTAATATTCCATAATAAATGTCATCTGGTGCCTCGGCTC
TCTGATTCTACTAAATTCCTATAGTGCGCGACTCTTCCTTTTTGCAATTT
CTTCATTTTTTTTCTAAACTGGTATGCCAGTTGGTCGGGGTTAGCTGTAT
CTATATGTCCTTTCCTGATTTGGTTGTTTTACTTCAAACTCCTTATGAAA
ATACAGTGTTATAGAATCTATAGCTTAGAATAGTTTTATTCAATATCGTA
ATAACAAAACTATGCTAATACTCCATCTTTGTAGAGGCAGTTATCCAGTT
TTAGATCATTATTGAGTATCGAGTTCACTAATTATGTCTATCACACTCTC
TGTCATTATTAACTGATTCATGTCAGTCTTCGTAATAGTATTTCTGCCAT
AAATTTAGTGAAATAAGTCTCATTTTGGGACTTTGAACAACATATAAACT
AAGAGGATCAATGTAATCTCTCTGGCATCTAGTTCTGATAATCGATTGAT
CGGGAGTGAAAATGTTTTGTACATTAATGTGCATCAGAGGATTACTATCT
TATGTTTTCGAGTAAGTTACTTTTATAAGTCATCTCCAGATGTCAGAAAA
CAGAAGTGCACTTTTGTTCATAATGACTGATTTAGATGTCTCTAAAGAAC
ACGAAACATGTCCATGCTATTGCATATTTTTAGTACTTTCATTTGTCTTC
GAGTCTGATTTTTCCATTATCAAAAAGTTATGAAGTAAGGTGTCTTATAA
TTTTAGGATTACCTTTCTCACTCATAATTATGTATTGGAATTTAAACAGA
TATAATTCTTAGCAATGAAGAGCTAGCTTCTATTGAAGAAGAGAGGACGG
AGGGTCCATTATGCTTTTATGAAGTGCTTGCGGATCATTTTGTCTGGGTA
CCTAAGAATGGAGAACCTATTCTTGATCTGATTGTGAAACTCTGGAGCCA
AGCATTTGCGTCTCATATATTCTCCCTTCTCTTTCACAAATGGGTATGTC
GAGTCATTTATATTTTTCTTTTGATGTTTAAAAGTTTTTTTTGGTGTGTC
ATTGTTAGTATTTAGTAGTGTCAAGTGTGTATTGAGCATAAAGAATTTAA
ATTTGAATGATCAAGATTAGTACGTGAATATAGAGAACATGAAATCATTG
TTATACGACATGTCAGGTTCTGTTTTTAGTATTAGTATAATGAAGAATTA
TCCAGACTTGACATTCTGATGAGCATTAAAAAAAGGGAAACCATAATAGT
GCTTAAACTACTCTAGATGCAATGAATGCATAGTGTAGTGAAAAAGTATT
ATATTAAACCACTTTATTAGTAGTGTTGAAGGTAAAGTTGTCAACGGGAA
ATGAATAGCTTTTATTTTATCACATTAGTACTTAATGGGCTTATTAAGAA
CTTTGCATTTAGGACACTTTACTGGGCTATACCTGTGATATGTATCTGTC
TTTGCCTAGTTGTGAACCCTTTTTAAGTGTATACTTCTGCATGAACAATG
TCCATACATCTCAAGGTTTTGCATTAGAAAATTCAACTTCTGTTTCATAG
TAATTTGATTTTTCACGCTGTTTAGGAATATTAGTGTTTATTTTTTTTTA
TGTCAGTGACATATAAATCTGTAGGCTAAGAAGAGATGGTCAATAAACAT
ATGAAGACTGCTTTATAGCAGGAAGTTAGATTTGACAACCTTGACAATGA
GCTACATTATAGAATGTCTCTTTTTTTTAATGCTTGTTGCAACCTTGAGC
TGCATATGAAAGTGGTTTCAAGAACTACTTTATAATAAATGAAGCTGGTG
ACATTTTTTTCTATAAAGTTCTATAAGGAATTTTCCGTCTCTGGACTCTG
GAAGCTTAATGTCAAGTTAAAATTTTCTTGTCTGGAAGCTTAAGAACAAT
TTTATAGCTAAATCTTATTTATTTAGTAATTTTTAATATTCAATCACCCA
TCCATTATGACTTGTAAATTAATTTGACTAATTTGCAACTGAAAGAAAAT
GTATTAACTAATACCTTACCTATTTGTAATCTATTTATTTGTGGGTGCAA
CATTGCAAGAAACTAAATGAACAATTGACTTCAAAATGTTTGGGAATTGA
TGTTGATTATTTGAAAGAGTTTCTCTTGACTTCCTGTTTACTACTTACGC
CATAGTTGTCGAGGTGATACTTATGTCAATGCCTTAGCTACCAGAAATGG
GAATGTGTTCCTGATTGCTTTGCATCTAGTAGGCAGGGTGTCTCTTTAAT
TATCTCCGATACTAGAGTGTCTGGGACAGAATATTCATCTATGTTCACGT
GTATACATCTTTTCTTCCCAACTCAACTCTACTTCCATTAATCTTGTTAG
TAACAACTATGTTCTTTTATTTAATTCTGTACCATCTCATTAAAAATTTG
ACTGCGGACTCTTTACATGCTTACAAATTTATTTTTCTGAGCTCTACTTT
TAAGTGAAAAACTATTTCTCATGGCTGTACTGTTTCCGGTGTTTTTTTTT
GGTGAATCTTCTTTCTTATATGATTAGAAATGAAGAATTCTTAATTTTGT
TTTTGTTAGTATCCAATCTTTACAGTTCACATAAAATTCTTCACATATAG
TATTTTTTATAGTACTTGTTAATTATTTACTTTCTATAATGACGACATAA
ATATATTTTGTTAATTAGCATAGATAGTTTAATATAATGATATGTTTGTG
TGCTTGACAAAAGAGAAGAAGATATATTCATGTATATATTAATATTATAT
CCTTCAACTCTTTAAAGGGATACGTAGACCAGCTAGTATTTAGACTATAT
GTTATTTATTAGAGGCGGACCTATCGAGTCATGAGGGTGATATCACTGAT
ATGTGGTGTTTTCTTTACATATTTTAGAAAAATTTTAATTACAAAAACGT
AAATAATTACCCTGTCTTTCAAAGGTTAAAGTGCAACCTTGCTCTCCTTT
AAGGAATTATCTACGCCTACTGATGATTTATGATAAATGGTCGAACACCT
AATTTACCTAATGGATGGCCTAGGTAAGCACTTTTTGTCTTGTCGTCCAG
GCAGCCTGCCTACGCCTTTACAACAAAGCTATGTACGTCAATGCCATCTT
TACAAGTTGCACTGAAATTAATGATAGTCACTATAAATTCTATAATCATA
CCCCCTTTCAGATTGTGATATTCCCCTGATCTCTCTTTCCGGTAATTTTT
TTTCCCAGTCATTGCAGTTTTTTGGTATTGGTCGCGATTGAATCAATTTG
AAATTGGATTTTAAGTCCAATCTGTAATTCAGATAACATGTATTGCAGAA
TTTGCAGTTAAAACTCGTCACAGTGTTTTTTAAGATGTCAAGTTAGTAAA
GATCTTTTTTTTTTTCCCGAATGAAGCCAGATCACAGAACTGAGCAGCTT
TTGCAATTTTACATCTGCAGTTATTAAATTAATAGACTTAGATAGAAAGC
TGGCGCAAACTGAACAGTGGAAGTGTTACTTATGTATAAACAGGATCTAG
TGGATCCTTTTTTTTTTTTGGAGTTTAAGATGTTGTATAGGACTAATAAC
ATACTTATTTTTGAAGAATTAGGTTTACTATTACGGTTCTTGCATGTTTA
TGTTGATAATATTGTACTTGTGGATAGTTGAGGTGTAACTATTCTTCCTT
GTCTGTTCTTGGTGCTTTGGATACCGTTAACTATGCATGATTATATTTAT
ATACACATTTCCTGTCTCTGTTCTCTTAATAATTTGTTGTCATTTATTGA
ATTCATTTTACTTGTAACCTTTACTGGCATCATTCACAACAATTCGTATG
TATTGATCTTATAGAGCTGGTTGTCTCACACTTCTACCATATATAAATAT
CATATCTTAATTTTATCACCCATGATAGACTGATAGTATAACACTTTGTA
TGTTGTCATAAGAACCAACAGTATATCATGTAAAAGGTATGGGAAATAAA
CATATAGTGGCAAGTTCGAAAATGATTGTGAAGTTTGAGAATGTAGTGAA
TGACATTGCTATTTGGGATGCTGCAATCAGAAGTTAAAGCTATAGATATG
TATATGGATTTCAGGATTTTGGAACTTTTGCACTAATCCATGTCATTATT
GTGTGTCTTGTCTATATTACTAAACCAAAGTGGAGATATTGAATAGTTTC
CTTCTTAACAGTAGGTCAGTATATTCTTCATGCTCAGAGTAAGCGGAATA
ACGATACTTGTTATCATTGCAGTTATTTGAAGTTCAAATTGATAATGCTG
ATGTCCTCCTTCGCTACTCATCAGCTCTTGTTCAAGGAGCCACAAATGTT
TTCTGGTAAGGAATTGTGTACTGCATATAGTAATATTTAAAATTGGTTGG
ATAGCATTGAAGTTGGCCTGTCTGGAATCATGAAGTGGTGCTTTGCTTAA
AAGCAGTAGTGATATCATTGTTTTTCCTTTCCATCAGCAACGTTATTTTC
TTTTTAAGATACGGGGAGAGGAGAGTGAGGATTTGAACCATGTTCCCCTT
TGTAATGAGTGAGAGTTGCCTTACCACTAGGCTAGACCCTCAACCTTCTG
ATTTATAATTACAAAGTATGAACTTGCTAGAATAGTTAAATTTTCTCTCT
CGTGTGTCCACTTACTTTTTTTTTCATTGCATATATATGATCTGATCTTT
GTTAATAGAGAAGGCACAATACCTACTAGGTGCTATGCTTTATCAGTAAA
ATATTCTATATGGTACTTAGAGATATCAGGTTAAGACACCATTAGAAAAT
TGTTCTGCATAAAGAGGGATGGAAAGCTCTTAAAGTCTAATAGTCCAGCA
AATTAGGGTGCATTAACAATTTGTTCACGGGCTTTTATGATTTATCATTT
CATGATATCTGTATTCACACATTTGTATTTATATTAATAAAAGGTGCACA
GATTTGTTCTTTATTACTGCATGGGTCTACTTGGCTCAAGTCCCTGATTG
TATAATAACTTCTAAATTATGTATATTTAATTTGCAGGATTGATGTCCAG
ACAAACACAAGACACTTCCATAGTCTCTTTCGGGTTAGATATCTTTCCGA
GTAAGAAGTTTTCAGTTGAGTAATTCGAAATTTGATTATGTTTTACAAGT
AATATTTGATTCATTTCAGTATCTTCTTGAAGAAGTTGCTTTGGTGCCTG
AACGGCTAAAGAAAATTCCATTACAGGTCAGGCATGACGGACATCTCCAC
ATACACCAAATGTAACTGATCTTACAGTCAATTTTTAGTAAGAACTTTTT
GCAATAGTCTTAAAATTATTGTTTTCTTTCATTTATTCAGGCACAACGTG
ATCTATTTCTTCTGCTGTCAAGGTTCATTTTCCTGTACAACATGGGTATG
CATGTCACGTTGTCACTACTTCCGATTTAGTAATCAACCTCAAAATTGCT
GTCTTTTATATCTTCTAAAATATTCTTCTTGCAGTTGACAAGATTGAAAG
TTTTTTAAAGAAATTTCCAGAATTCCCAAATGCTTTCTTGATTGGGGGTC
CAGCAGATATCTTTGTAATTGAGCTAACTGATCAAGTAAGTTAAGAATGA
ATAACATCTCTAGTAGTGACCATATTAATGCTAGATGTCAGGGATACCCT
TATTATTTAATTTCTAACCAATTGTTTACAGCTCTTGAAATTAAAGGTGG
AACCGGTGCTGCTACACTACCTGTCCCACATCAAAGCTCTACAGGGTACA
AACTGAACGTTCTATGGGAATTTGATTCTAATTTGTAAGTCACCTGTGGG
GAAGAAATAGAAAACTCAATGTTTATTTTGTCTCCAGGTATGGAATTGAG
AATGGCTACAAGTACTCGACTGAAGACTTGCTTGTATAGCTTCACTTCTC
CAGGTGGTCCGATGTATCCAACAAGAGCTGTTCGTCATGCTGCATGGGTT
GCATTGGACTTGTTATTCCCTGTGAGTCCCATCCCTCTGACCCTTGCTTT
ATACAAAAAGGGGAAGTCCAGTAGTAGGAGTTTGTAGTATATGAGTTTGC
TCAACTTTTCATTCTATTCATATGGACATTGTTTAAGTAACAGTTTGACA
TGTTGGTTCAGGTTGGGCAGTATCCCCGACATGTTATCAGTCTCTTCTTC
CGGTTGTTGTATCCATGGTACTGGCCGTCGTCCTGCTGGAACTTTGTAAT
ATCGTGCGTACAGGCGGTGTTTTATTCTGTGCTAAGGTTGCTTTTCTCTA
GTTGGGATAGGTTGACCAAAACGAGGCAGGCCTAAATATGTAGACAGTTG
AAGCTTGAACCAACAGTAAAATGTTATCAGGCCATGATTCTGAAACTTAA
CTAAAAGTTTGTACTTTGATGTAAATCTGTATGATTTCTTTTATACTTTC
GTCTTAAAAGTGAATAGTTGTCTTGAAAATACCTGTGGCAGACAACCTGC
GGATTCCTGTCATCGACAGCAACAGTGTTCTAATCTTAAGCTTGTTGGCT
GTTTGCCATAAAATGTTTCTTAAAAA
Sequence Length: 
7676
Sequence Checksum: 
482571971f21af3833b9102664f69afb
View location in JBrowse: 
DCARv2_Chr5:34173681..34181356-
Gene: 
LOC108220639
Gene Biotype: 
protein_coding
Gbkey: 
Gene