LOC108202950

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108202950
Identifier: 
LOC108202950
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017371589.1, is a part of gene, LOC108202950.
The genetic_marker, MK001124 GSSR-125, is adjacent to gene, LOC108202950.
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_017371589.1XM_017371589.1mRNADCARv2_Chr9:11510769..11520278
Sequence: 
AAGTCTGCAAAAGAAAAAGAAAGAACCATCTTCCCGCTGCTCTTTATCAT
TATCGAGTCCTGGTCCACCACATTCACACACACAAAACATCTCTCTCTCT
CTCTCTCAACCACCGCAGGAAAGAAAGATGCAGAGAGACGAGTCAGCTCT
GAACACATACAACTACGGGGACGCGTATTACTGGGATGCGCGTTACATCC
AAGAAGCCTCCGCTGGTGGAGCTTTCGACTGGTACCAGCGTTACTCTGCT
CTCCGTCCTTTTGTTCGTAAATTCATCCCCACTTCTTCTCGTATACTCAT
GGTTGGCTGTGGCAATGCTGGTAAGTTCACTATTTATCATTTTCACCTTT
TTTTTTCTCTGTATATATGTCAAATTTTAGAAATATAGCTGCTTGTTAAA
TTTTAGGGTTTAGTTTATATAGATGCGATCATGTTCAGCTTTCTGTGGCT
CGAGAGTTTGGAATTCTGCGGTGATTTGATTTGCTTAGGGTGGTGATTGG
ATTATTAAGTGATACTAGGTGTTTGTCTTTGATTCGATTAGCTTTTGACT
AAATTGAAGCGGTGTTAATTTAATTGACTGATTGGTGTTTTTCGTTTGAT
TACTAGACTGAGTTTGTGTTTATTTGGTTGAGTTTTTAAACACCTTGATG
TTGTGAACACTAAAGCTCTGCAGCTCGGTTAGGTTGGAATGAATGTTTAC
AGTGGGAGAAGTTTTTTTGTTTTTGAGAAAAAAGGTTTTTACTTTCTCGA
TTCAATGGAGGTCAAACCTACTGATTTGAGAATCAATTCTCCTATTCTCT
TTTGTACTCATTTTACTCAAATTCTTTGTCAAAGAAACTTTGCTCTTTCA
TTGTTCTCCACTTTACATTCTTACTTTATACCCATTACCTCTTTAGTTTT
TTCTCCCCACAAATTTTAGTTGATTTCTTTCAGTCTAACGGAGCTACTGA
GATCAAATGAAAGCACCTACATATAACAAAAGGATATCTTCTGTAATTAC
AGATATTAGAAAGAAAGTGTATAAAATTCATTATTATATAGTACAAAGAA
GCTGTGCTATATTCTAATTTAATACATGAGAGGATGAATTCAATTTACTT
TGATACAAACATCTACTATTATTATCACAATTTAAAAGAGAAACATTTAA
AACGGAAGTACAGATGAACCGGAGCCTTGTACTAATCTATAACTCAATTA
AATAAATTAAAGAGCTAGAATACTGAGGAAAGAGTATGGAACTGAGTGGT
GTAAAAAAATGCTTGGGGTGAAACTGTGAAGGCCATAAAGAAGATTGGAA
GTTGTTATAAATGGGTTAAATTGTGCAAGGACAGGGTTTTTTATGTTTTA
TTGCGGTTAGTTGTCTAATACTTAAGTGATTTTGAATATGGGTTCAAGAT
AAGCTAATATTATATTAAGTCAGCTCTTTCACTCTGATATCTTTTACCTA
GATGTAGCACCTCCAGGGCCCCTCCCGGTCTTGATAATTGTTTCAATTGT
TCTATTGGTAGATCTATAGAAGCTATGTAAGCACACAGACATTGAGTGGG
TCTCTCTTGCTAAAATGCACCTCGCATTCCCACCTCTCCCTGTCTCTTTG
TTTGCTCCACCCCAGGAGATGATGTAGAAATTAAATGTATCAACCCTCAA
CTAAAGTAGCATAATGAAAACCGTGATGTTGGTCCAACTTAAAGAAAACT
AGGAACTGAATCTCTTACGAAGGCCTCAACATCTTTTCTCATAAGAAGTG
ATATCATAGATGTTCTGTATACTTTCAGTACTCATTCGAGTTGCACCTGT
TCCACGCACCATAGACGTTGCCATTTGGTATACCCCTATATCAAGAAGAA
ACATTAAATATATCTTTTTATAGTAAATAAATATGTTGGTACCCATTTGA
AACTGTAATGGCAAAAAAATCTGTAGCTATTGTTAGATTTGTAGTACAAC
TATATAAGATACTAGTAGGCAGTAGCTCATACTTGCATCATGTTTTACAA
ATAACTCCAAATTTTCTAATCACGTAGTTTATACAATTGAATTTGCAGAT
TTCATGATTTCAATAACATTAATGGTGGGGTCGGTATGGCCTATGTGGAA
TGTAATAAGTTTTAATTGCAAAGTAGCTAACTTTAATAAACTAGTTATGT
GCAACTCAAGGATTATGAAAAATTTACCTTGTTGCTAATTTATGTATGGA
TGGGGCATTGGCTTGTCCTTTATTCACATTTTTTGTTGGTAAAACCTGAA
CAAAGACGGCAACAATAGTTTTTAAGATATGCCTGAATGATATTTTGTTA
ATGTGAGGTTCTCGTAAAATTAGAGAACTGTTGCAATGCTTTGATATGTG
AGCCCGAGTAAATTTCTTGCTCCTAGCAAATGTTTTTTTTAAAGTTTTAT
GGCTTTGTCCTCCAATAGATGACTGCAGGGAATGTTCCACAGCTCCACTA
GAACCAGAAAAACATAATCTGTTACTTATGAAAAATTTCACATTTAAAAA
TCTTTATATCATTACTTACATTTGGTAGATTTCAAAAACTAACAATTTTA
AAAGTTTTAATAAACAAGTGCCCATATCAAAAAGTTTCAAATAGAGATGG
TAAGCATGTTTTTGTGACATCTAAAGAAGGTAAATTCAGACAGTTGCGCA
TATAGTGGTGATTGAGTGCACAGGTTCACGTTCAGTCCTTTTTGAATTTT
TTAAAAAAAATTTATTATATCAATTAGAAAAAGGTAGAATTACTACTGTT
AGGTTGGCTACTAGTATACTAAAAATCTTTATAATTCAGATTCGTGATGA
TTATTGTTTGTCCTAGGCAGACGTGCACTATGATTCACAAAACAAAACAA
TGTAATAGAAGCAGTAATCAGGAGAAAGATATTAGTATACTGGTAGCCTA
GCATTAAGATTAGTGGTGGGCTAGTAGCCTACCAATTGGTAGTTGCACTT
TCTTCTAATATAATGTAGTAATATAAACAATTTTGAATGTGAAAAAGAGG
ATTAGATATGGACCCTGGGCTATCAATTGCAGTTCACAACCCCATCACAG
TTTGGCTGTACCATTATTGAATGTCACACAAAGGTGTTCACCATTTCTAT
TCGAAACTATATAATATGAGTACTTATGTATTAAATATTTATAAATATTA
TTCGTAGGAATTATATTACATTAGTATTAATTTAACTTCTTTTAAAATAT
TAAATTCCTTGAAAATAATTTGTTTACCAGTTCCATTGGATTATCCTCCC
GAGTTATCTAAAGGAGGACAAAGTCACAAAGTTTGAGAAACATTCGCAAT
GAGGAGCAGGTAGTTTAATTGTGCACATATATCATTAAAGCAAGAAAACC
CATTCTTTTTATTGTTCAAGGGCCTCACATACTCAAAATATTTTCTAGGT
GGATCTATTAAATACTGTGTCCATTCAGATTTTTGGATTGTGTTGGATTT
ATGGTGATTTCATGAATTTGTTATAATATTGAGCTGCTAAGGTAATATGA
GTTTGTATCTTTGTAGTTATGTCAGAGGACATGGTTAAGGATGGATATGA
AGACATAATGAATGTGGACATTTCTTCAGTGGCCATTGATTTGATGAGAA
GGAAATACGAGCATATCCCTCAGTTGAAATGTATCCTAGGATGACAATTA
TATTTAAGTCTTTTAAATTATTATCTTTTGTTTTTTTAATGATGAGTATA
TGCAAAATGATGAATTTTCCTTATAAAAACTTTGAAGACATGCAAATGGA
TGTTAAGGATATGAGCTTCTTCCCTGATGAATCATATGACAGTGTCATTG
ATAAAGGTAATTGTGCGCACACATGTTCGGTTACTACATGTTATGCGAAA
AATTAGAAGTTGACCTTTTTCTGTGTGTTTGTGGCTGGCCTGTGTTTTCA
TGCTTGATACATGGATCCAGGGACTCTTGATTCGCTAATGGTAATTACTA
ATTTGGTCTTATCTCTGTATTTCTTGATTATTGTTAGCAGCATTCTGATT
TTTATTTAATCTTTTAATTTGAAGTGTGGTACTGATGCTCCAATCAGCGC
GGCACAAATGTTGGGGGAAGTGAGCAGGTTGTAGGTTTCATGAGCCGTTA
AAGCTAATTGATATCCTGAACACAACCAGTTCTGTTTATATGCTCTTTTT
GTTCTTTGCTTGCAGGCTTCTTAAACCTGGAGGAGTTTATATGCTGGTAA
ACGGAATCCTGCAAAGAATGCTTGCTTTCTCTGCTGCTTCCTAATATCTG
AGCTCAAACCAGTACTTTTTTTCTTTCTGTATTTACAGATAACATATGGT
GATCCTAAAGTAAGGGTTCCTCATTTGCGCCGACCAGTATACAACTGGAA
TATAGAATTGTACATCATACGTAAGTTGTGTTCCCCTTTTATTCGATTTA
ATAATGCAAACTATATTGTTTTCAAAATGCAAAATTTTAGTGTATTCACC
AGAAACCTAATTTCAGATTTTGTTGGTCATATGGCCATCCTTTATTTTAT
AATATGCCTGTATGCAGAGTAGAAATATAGTGTCAAGCTACACGTGTATG
TAGCAGTTGTGCGATATAATAATTTTGAGGAGAGTTAACACCAGTTGAAG
GGGACAACATAAACACCTACAATAATATAGCTCAAGGAACATTTCCTATT
ATAATTCTTTAATATGCTTTTTAAATGTTCTCCACCTCCATATATCAAGA
GGGTTTTATATCAAAGTGATCACCATTGTTATCAAGTCGACGACTAGTCG
ACAAGTCGTTTTATTGAAAAAGTCAAGCAACGACTTATTTAGTCTGGCGA
CTTATTTTGAACATGTCAGTGTCTCCCTAATCTTTGTATCATTTTAACTT
CACATTATTATTTCCTCCCTGTTACTACTTTTTGGCTTCAGGCTATGTAA
TCTTTGTATCATTTTCAACATATAAGTATATCCCTAATCTTTGTATTATT
TCAACTTCACTTTATTATTTCTTTCCTATTACCACTTTTGGCTTCAATTT
CTGTGTGAACTAACAATCTGCTACGTCGTATACATCTCACTGCTGTTTAT
TATCTTTTACTTTTGATTCACACTATAAACTGATGTGCGTTCAACTATAT
TTTGCATATCAAATCTAGTAAAAATATATATAAGAATGACTTGTCGACTT
TTTACGACTAGTCGGGCGACTTGTCGACTAGTCGATTCCAAGGTATCCGG
GCGCCGAGGCTCGACTTGGCGTCGTAATAACCTTGGTGATCACCATTATT
GTCAAAATATCTCACCGAGCAACCAAATGTCCACGAGGACTCATTTAAAG
AACTCAAATCACTATGTTAAAATTTTGGCAAAACATCGATAGAATAAGAT
TTTTTTTATAGTACATTAATCTTTTAGACATAGGCAGTTCAAGATTTTCG
TTTTGATGTTCACTAAATCAAGTAGGAACAAATTAAGGTTAAAGAGTTAC
GAGAGAATAAAAAAACACATTATCATGTTCATGTATGTGTTTTGACACGT
TTCCACATTTATAATTATGATTTCTTTTTATTATATATATAAGCCACGTG
TTGGACACTTCATCTTGAGACTATAATTCCCTTATGTTTTTCTGATAATC
TTTTTTTAAAATTAAGGTAGTGATATTTATAGTGATTGGAGTGTTTGAAA
TGAGTTCCCGTGGAGATCTGGTAGCTAAGGGAGATATTTTAACGAGATCA
ATGGCCACTTTGATATAAAATCCTATATCAAGATGTCACTAAAAAAACAA
AGAAAATATTCCTAGATATGGCCCCGATACCTAATTTATTAAACTGTTAA
AGTTGCTGGATCGTTAGAGGCCAAAAGGTGTCGGTGTGTGTACTGACAGC
TGTTTTTCCAGTGTCCTGCTCTTCATTCTCACAATCTATTTGGTGGTATG
TGGTATCCAGGCTGTAAGTCAAAGTTTGTGTAAAGGTTGATTCTATGAAG
CGCGTCCAACAGATCCTGCATTAGGAAGCTAGGAAATTTATTCATGATGG
TTATGGATTTAAGCTTTTTTAACTTAAAAGTAACATCCAAGTTTCAGTTT
TTTTCTTTTCCATAAAGAGAGGGGAATCTCGAGATGAGCAACTAGACCCA
GTGATCTCCCACAGCAGTATTTCCTTGCACCACCAATCAATTTCATTCTT
CTGATTAAAAGAGTACCTGTAAGGTCTGGAGAGAAGTGATAAAACCCTTT
TATTGATTATTCTATAATAGGCTGGAAGACCTGTTAGTGCTTTAAAACAC
CTTGAAATTACTAAGAATATGTGCAGTTGCTGTTCAAATTCTGGTCACCA
ACTTAAAGTAGCTTTAAATTGTAATCCCTTATTCCCAATTTTTTTTTTTT
TTATAATCTAACTAGGAGCCTGTTTGTCTCCGGTTTTAAGCCGGGGCTTT
AAACTATTTATAACTTTAAGTTGAAAAATGTCTGTTTGTGTAAGAAGCCA
GAAATTGACTGAAAGTCAGGAATAAGCCAGAAACTGACTTAAAGTCAAAA
TTTAGTTTGAGGTACTTTTTTCAGTGATGTAATTTTTTTGAATTTTTTTT
TTTTTTGGATAAAAGTCGCCCATAAGTGATAAGTTACTCATAAATCACTT
TTATTTTTGTTATTACATTTTCAATAACCCATAACTCATAAGTCATTAAT
AAATCAAATTACCCAAACAGACATTTAAACTCCCAACTTATCACATTAAG
TCACGTTAAGTTGTAAGTCATAATTTTAAGCTCAGCCAAACAGGCTCTAG
ACCACTTACTGAAGAAGCATCAAATCTTTGGTCAGGAACTAAAGTTTTGT
AGCTGTATAGGATGGTTTGTGTTTCCCAGTTTATAGAATGCAGAAAGGAA
GATATTTGCAGCAGAAATATAGGGTTAGGTAGACATGAAAGAGAAATAGA
GAAGAGAGAGAACAGAGAATCAGAGAGAGAGAGAGTTCAGGCAGAGATCA
GAAGGGAAGATAGCTTATTAAGATTAGTTACTTTCTGAGAAATAAACATG
GGGGTGGAGGTGTTGGGGAAAGAGGGGGGGGGGGGGGGGGGTTATTTTTC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNGGGGGGGGGGGGGGGGAGGTTAATTTTCTGATATTAAA
ATAGATAATCTGAAAATACACCCATTTTAACTACCTCCAGGGAGTAACCA
ACTCAAAAATTACTCAAATACCCTGTACTGCTGCATAGCCTATTACTAAT
TCTTTGGTATTGCTCTGCTCCAATCCTGACACGTTTTTTCATTTTTAAAG
AACTTCTGGAAGACTTTTCTGCACATGTTATCCTTGTAAATGTTTTTTTC
GCTAACATAACTTATTAATGTTTCACTATGTGGTTAATTTCATGGGAGCT
GCACAGTGGACCCTGGTGTTGAAATTGTATCTTAAACCTGAAAATTAAAT
GACCTTGTGAACCGTGATGGTTATCCATAAAACTATATTTGGTGTCTTTG
CAAGATCTAACCAGCCCAAGTGCCTGTACTAATGACTGTCTAGCAGATTT
ACTCTCCTCTTAGTGTTGATGTACTTGTGCACCGTATGAATTATCCTCCT
TAGTCCGCTCATATAGTAATTTTTAAAATACATAATCTGATAAAACACCC
ATTTAACTACCTCCAGGGAGTAACCAACTCAAAAATTACTTACTACCCTG
TACTGCTGCATAGCCTATTACTAGTACTACTTCTTTGGTATTGCTCTGCT
CCAATCCTTGCACGTTTTTCATAAAACTTCTGGATGGCTTTTCTGCACAT
GTTATCCTTGTAAATGTTTTTTTCGCTAACATAATTTGTTAATGTTTCAC
TGTGTTGTTGATTTCATGGTAGCTGCGCAGTGGACCCTGGTGTTGAAATT
GTATCTTAAACCTGGAAATTAAATGGCCTTGTGAATTGTGATGGTCATCC
ATAAAACTATATATGGTGTCTTCACAAGATCTAACCAGCCCAAGTGCCTG
TACTAATGACTGTCTAACAGATTTACTCTCCTCTTAGTGTTGAAAAGGTT
GTCCTAGTGATATATAAGGCATCACTAGGACTTTGTTGGATCAACATTTT
TTTTTTTTAAATCAAATGTCCTAAATTATAACTTAGGACATCATATAAGA
CATCTGTTGGACTTGCTCTTAAGTAACTGAGTGAAGCTAAGGTCTGTATG
AGTTGGAATAGGTCACGCTTTAATGCAAGATTGTCCTCAATAGTTTAATA
TGAGATATTATTAGGCATTTTTGTTCCAATTCGACCTATTGCTGAAGTAG
CACTGCTGTTTCCCTGCAATGTTCTTGTAAAATGAAAAGTAACTACAATA
AAAATAAAACAAGTGGGAAGAAAAAGCAGCAACGAAATACTTATTTCTGG
TTCCTTTTTATTTCGTACTATCTGATTAGCAGAGGGATCAAGAAGAAACC
ACTATCTTATGGCCTCCATTATTTTAAGATGAGAGGACACACCCTATGTT
CACAAATGCTCTCCTTCGGAAAAGATCAAACAGAAGGATGTTTGACTGGT
TTTGTCCCAACTCAAATTCAGCACAAGCTCCTTTCCCCTCCTTGGGGTGG
TCTAGTTCGTGGCATGTTATGTACTTGTTATCTTTTATGGTCCAGTTGTT
GGATGTTATGTACTCATTAGCTTTTATTTAATTGCAATTTGCAGCTAGAC
CTGGATTTCAAAAGCTGGGTGATTGCCCATCATCTGCTAAATCTTTCCTA
GAACCTGTGCCTACAAATGAAGATGGCACACTTCATGCAAGTTATGTATT
GGAAGATCCAGATTCGCACTTTATATATATTTGTAAAAAGGCAGACGAAA
CATCTTGTATTAGCAATGTTCCCGACGGCTAATAATTTATGGTAAAGTTG
CTTGATCAACTACTATTAGCTGGTTCACTTGTCTCCAGGTTCTTCAGTGT
GCCCCAAGTTATACTTGCTTTCGTCGCAGCTTTTACTTGGTATGCTATGT
TGTTGATTAAAAGAAAATACCAGGACTTGTGGAACTTTTAGTTAGCATCT
TGGATTCATGTTTGTAACATTGTTGTATTAAGAAAGGCAGATTACATGTA
CATTTCTGGTCAGAAAGTCTCATCGTATGTGGTACATGAAGTTCTATACA
TTACTTTTAGCAAAAACCCTGTTTTAGGTTTTATTCGAGTAGATGAGCAT
TATTTGAAA
Sequence Length: 
9509
Sequence Checksum: 
edc4c6aced5d752b9535c00b178036b6
View location in JBrowse: 
DCARv2_Chr9:11510770..11520278-
Gene: 
LOC108202950
Gene Biotype: 
protein_coding
Gbkey: 
Gene