LOC108204961

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108204961
Identifier: 
LOC108204961
Cross Reference: 
NCBI Gene
Relationship: 
There are 3 relationships.
Relationships
The mRNA, XM_017374667.1, is a part of gene, LOC108204961.
The genetic_marker, MK003574 K1018, is located in gene, LOC108204961.
The mRNA, XM_017374668.1, is a part of gene, LOC108204961.
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_017374668.1XM_017374668.1mRNADCARv2_Chr1:4140932..4148107
XM_017374667.1XM_017374667.1mRNADCARv2_Chr1:4140932..4148106
Sequence: 
ATAAAGCGCGCTCACACACTCTCTCACTCCAACTCTCTCTCTCTCTCACT
TTCTACATGGGCTTTGTGTCTACCTCCGCCGCCGTGTTCTCAGTCACAAA
TCTTGAAAACCCACTTCACTGTAAGCCCCTTTGCGCCGCCGTTCCTCAGC
TCCATAGCTCTCCAAGAACCGGTTTTTCTTCAAATTGGGTAATTAATTTT
CATAAAGTTTTTACCTTTTTGCAAGAGAGTGTTGAAAATCTAATCTTTTT
GTGTTTGTTTGTTGTTGTTTTAGTGCTCAGCTGTGTTGAGGTTGAATAGT
TATCCAATTAAGGCTATGGCAGAAGCTGTCGATACCGTTTCTTCACCTGT
TGCTGCCTCTGGTTCCTCCGTTTCTGGTATATCTCTCTCCCCCCTCTCTC
TCTCTCTCTCACTCTCTCTCTCACAGCTTCTCTAGCATGGATCCTTACAA
GGTATGATCGGTACAAACCCTGTTCGTATATCAAATCATTCTTTTTGACT
TGCAATTTTTATCTTCGTTATGTATTCCTTGTTATCGTTGATGCAGCACC
GGGCATCAAGTGCTTTCAACTCTCCGTACTGGACCNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNCTCTCTCTCCCCCCCTCTCTCTCCCCCTCTGTGT
CTGTGTCTAGTTCCTCTTTCTGGTATATGTATATGTGTACATACTACATA
CAGCTTTTGGTAGTTTGTGTGTATATATTTAGACTAGTAGATAGATTAAG
TTTTGATACTTGAAGTCTTTGCATTAAAGTTTGAAACTTTTTATGCATTC
AGATAGATGAAGATTAATTCTTGAAATCTCTATATTGATGTGATTAAGTT
TTGTGATAATTAGTTTTTACTTGTTGGTATATTGTGGAAGGATGTGTGCG
TTCTCTTTTAGAGAATATTGTAAAATGTGCTCGTAGAGTTAATCTTTTCT
TAGGACAAGGAGATACGTCGTCTTTTTTCGTTTGTGTTTTACTTTGTTTC
CTGGTTTTGATAAGTGTTGATTACATCTATGAGCCACTGAAGTTAGTGAT
TAATAATTGTTTAGCAAATGGTTGGTGCTGCTACTACTCATTTCATTTGT
TTGATTAAAAAAAGTTCTTTTTTTTTGTAAAATTATTATTTCTTACGAAA
ATTAAGAGTAGAGTAGATTACTGGCATAATGCTCCTTACTACAATTCCTT
TTGGTTGCATTATATGTGTGTTTGTAATACTAAAACTGTATGTACTTACA
GGGAGCAAACAAGCTCTGATTTCGCTTTCAGATAAAAAGGATTTGGCTCT
GCTTGGCAATGGACTCCAGGAATTAGGGTGATTTGCGATGCCCAGTCTTA
ATGCAGTTTTTGTGTTACTTTCCTATTTCTTGTCTATGATCCCCCCCCCC
CCCCNNNNNNNNNNNNNNNNCCCCCCCCCCCCCCCCCCAAACCAAAAAAA
AAAAAGGAAAGAAAAAGAACATACACTATTATCCTATAGTAATATGTTTA
TTGGTCTTCCTGGGGTTCGATACAGAGTAGATCCCGATTCACCCTGCACC
AGTCTATTTGGTATGGTGTAACTATGTAAATGATTCTTCATCTGCTGATC
TGCTTAGTGGTAATGATATGTTATTTCTGCTGAAACTTAGATCTGCCGGT
TGACATGTGATGCGACAATCTGGTAGCTTAGAGACAATATTATTAGTAAA
TTTGAATACTTTGACACACTAGTGGACTGTATTTGTATAAATGGTTTTGA
TCATGTAATCTAATATAGTGAATCTGGAGCCTACATAAACTATCATATGC
TGATCTAAAGGCTTTTTAAGAGAAGCTCAGAACCATCAGCTAATCTCAAT
TGATTTTGTGGAAAGGAGACAGCTTTTCTAAATTATATTGCAAAATGCAA
AGTCGTTATCTTTTGGTAAGTAAAAACAAACTAGAATTGTTCCTTGGTAG
CAAGCAATGTGCGATTTCTCTAGTAGTATTGTTAAAGCTCTTGCAAGAGT
CTTGTTACCGCTCTTGATGACTTCATCTCTAATTCTCTACTTTGTAGATA
TAAAATTGTCTCGACCGGAGGAACTGCATCTGCCTTGGAGGGTAATGGGG
TGTCTGTCACTAGAGTGGAAGAACTCACCTGTTTTCCGGAAATGGTAAAG
CCAGTTCATATAATAAACCTCTACTCCTTTTTATTAATTGCTAACTTACA
CCTCAACTTACTTGCAGTCACAAATATATGTGTAAATATTAAAATAATGA
TGAAAATCTACTTTATTTTGTGCGAAAATTATCCAGGTGTTCTTTAATTC
CAAGTTCCTCTATTCATTTTGCCTTCATGTATGCCCTTTGTGTTAGATTG
TGGTATTGAAAAATCTATGTTCTTTCACAGCTTGATGGTCGTGTAAAAAC
ATTACATCCCAACATCCATGGAGGAATCCTTGCTAGAAGAGATCAAAGCC
ACCACATGGAAGCTCTTGATAAGCATGGAATTGGTGAGTTCTGAATTTAA
TGTTCAACAAGTTCATCTTGCCTCCCATTCTGTAGCCTCAGTTCATCTTA
GCCTATTTTGCATGACACTCTGCTGCAAAGCCTTAAAGAAAAACACATCA
TAATGTTTCATATGCTCAATCGATCTAGAACAACACATTTTTTCTTGTAA
TGTGCACATCATAATGCTCTTGTTACACTTTTTCTATCTACCACCATGGC
TGATTCATTTTGTCTTTCTACCACCTTGCCTTGTTCATTTTGACCTTGGT
TTTAAATCTGAATACCATTGTTTGGCATCGTGGGCTTCTAGTAATGTTTA
CTTCTAAACCAAGACCTGTATGTTGCTAAGAAACAATACATTGAGAAACT
AATATTTGCAAGTCAATAGTTTAGCAGTCTATTCTATGTGTAAGTTAGGT
GGGTAATGTTGACTAAGCAGTTGAAATTTATTCTGGGGTGCAAGTTTGTG
GCCACGAAAATAGACAATTATTTCTAGCCTTGTAAGTACAAGTGTAGTGT
TGGTTATCTGTGATTTTCCAACCCTTGTAGGAAAGAAACTAGTTAAGTTT
TCTTGATAGAACTATAGAAATAATAAAAGTGTTGGGTAACAGATAAATGC
AATATTCTTCCGTATTCATAGGTTTTTACGAGCAATGATTGTTCTTTATA
CAACAGCTAAGAATTTTCCCTGCAGGTACATTTGATGTGGTAATTGTGAA
CTTGTATCCGTTTTATGACACGGTTTCCTCAACCAACGAAATATCATTCG
AGGATGGAATTGAGAATATTGACATTGGTGGGCCTGCCATGATCAGAGCT
GCGGCAAAGGTTGTCTATCTCAGAAAAACTTCTCTTTTTGTAGTATTACT
GTTCATATAACATTCTCTTTTTTTGCTTCTTCTATCCTTTTAGGCACGTG
TATGTGTAACAACACAAAAATAAAAGAGAAAATAATCAAAATATATAGGA
GTCAATTTTGATTTACTACTTAATTCAGCAATAAGTAAATTAGGTCAACG
CATTGAACATATTTAGCCGTTTGATCCTTCAACACTTTGTTGTATTCCAT
TCTGTGATATGATGACAAGCTAGTATCTCATAAAATCATTACTAAATCAA
GTTACAGTATATAGAGCTTAGAAGACAATCTGCCCTTTTCCCTACTAGAT
AATAGAGCCTGTTCTGTTTCTCAAACAGGAGTGCTAGTTATTACCATATT
TATCAGCTTCTGGTCACTTTATATTAATTGAACAGAATCACAAGGATGTC
CTGGTGGTGGTTGATTCAAAAGACTATCCCGAACTTTTGGAATCTCTTAA
AGCAAATAAGGTCAATGAACAATTTAGAAGGAAGCTAGCATGGAAGGCTT
TCCAACATGTAGCTAGTTATGATTCTGCAGTTTCAGAGTGGCTTTGGAAG
CAGACTGAGGGAGGTAATTCTTTTCTTGTACCTCTTTCAATCTAGTTTTA
TGTCATTTGTATTTTTTATATAAATTATAGATATAATTAGCATACAGAGG
ATGAAATTTCGAAATAATTGTGCATATCCAGACTAAATATTGAACTATCA
TTAGGAATAATAATATCAATGTATAAATTTGCTCGCCATTTTTGTGAAGA
TGAGTCAAGGAATGTCAATGTAATGGGGATAGGGCAAAAATGTATTGCAA
AATATAATATAATACATACTAATCCAAATCTGTTTTAGAGTGTATCAAGC
AAGGATGTTTGTGATATTATAGATCTCATAATTTGATTTAGTATACCTAT
GAGAGACATCAGTTATATCTGGTTCCTTGTAATTTATGAAGCACGTGTTC
TGACGGGCTCTATTTGGTAACAGAAGATAAATTTCCTCCCAGCTTAACGG
TGCCCCTTTCTCTCAAAAGTTCTCTTCGTTATGGTGAGAATCCTCATCAA
AAGGCTGCATTTTATGTTGACAAGAGTCTTGCTGAGTTTAATGCGGGTGG
TATTGCAACTGCTATTCAACATCATGGCAAGGTGAGACTATAATGTTATT
TACTTCTCTGACCTTTGTTGTAACACTCACAGGATTCACTGGTATAGTAG
TTTGAAAGTTATATATACCACACACCCTGTCAGAAAAGAAGACTATTTTT
GTTAACATTATTGGCAGTGAGTATGAGTATATGTGTGTGTGTGTGTGTGT
GTGGTGTACATGTATATATTATTGCAGCTAATGATGTGCGATACAAATTT
GGAATCAATGTCAAGTAGATGTTATTTATAAATAGTGACAACAAAATTGC
AATTCTTGGTTGAACATTGAACTTTCTGCAACTCTGTCATATTGTTACTT
AAAACTATGTGACAAGTCTTGCCACCAATTTTCTCTGTTACACTCATTAA
AATTAATAATCTGTATAAGGTATGTTCTCTTCTCATTGCCAACATATTCT
TATATTGGTGCAGGAGATGTCCTACAACAACTACCTAGATGCTGATGCAG
CTTGGAACTGTGTGTGCGAGTTTAAAAAACCTACTTGTGTAGTTGTAAAG
CATACAAATCCCTGTGGAGTAGCTTCGCGTGAAGATATAATTGAGGCATA
TAGATTAGCTGTAAAAGCAGATCCAGTGAGTGCTTTTGGTGGCATTGTCG
CCTTTAACATAGAAGTTGATGAGGTTAGTTTGCTGACATTATAAATTTTC
ATGGGGCTTTTTTCTGGTTAAGGTTGCATGCTTGCATTCCATACAAATTT
CTTCCTACACTACTCCGTAGCAAGAGGAAGGGTCCACTGCAGTCATTTGA
AGCACACTTCACACTTGCATGCACACGTATGACTGCGAACACAGATTATC
AATATTAATTTCTTACATCCCACTCCAAGTGGAGATAAGAAAATAATTTT
CTCTGTAATGCCTTGAGAAGCTACGAGTGATAGGAAAAATATAAGAATCA
AGTTTATGTATCGTTGCATCCTGATGTATGATTTGATCTGTTTGGCAGGT
TCTTGCCAAGGATATTCGAGAATTCAGAAGTCCCACTGACGGAGAAACTC
GAATGTTTTATGAGATAGTTGTGGCTCCTGGATATACACAAAAGGGGCTA
GAGGTTCTTCGTGGTAAGTCCAAGACATTGAGAATACTTGAGGCTAGCCA
GAATAGCAAAGGGAAGCTTTCACTCAGACAGGTTGGTGGGGGTTGGTTAG
CTCAAGATTCTGATGATTTAAGACCAGAAGATATACAATTTAAAACAGTC
TCTGAGAAGACACCTGAAGAAAGCGAGCTTCATGATGCAGAGTTTGCATG
GTTATGTGTGAAGCATGTAAAGAGCAACGCTATTGTAGTTGCAAAGGTAA
AACCACTTTCTGAACCTTGCAATAACTATCTTGCAATCTTCTTTCGGTTA
CTATATACATGCTGATCATTCTTTCTCTGTCACAGAATAATTGTATGTTG
GGCATGGGAAGCGGGCAGCCAAACCGTGTGGAAAGCTTGAGGATAGCTTT
AAGAAAAGCTGGAACTGAGGCTAAAGGCGCAGCTTTGGCTAGTGATGCAT
TCTTTCCATTTGGTAACTATATATTCATGAATTAGTAGATATCTGAATGT
AGGGTCTTGTGTCTGGCTCTAATCCAGCCTTGTTTCTGTAAACAGCTTGG
AAAGACGCAGTTGAAGAAGCCTGCGAAAGTGGAGTTGCTGTAATAGCAGA
GCCTGGGGGTAGCATAAGAGACAATGATGCAGTTGATTGTTGTAATAAGT
ATGGAGTTTCACTTCTCTTCACTAATGTGAGGCACTTTAGGCATTAGCAG
AGAAGTGAATCCATCTATTCCTTTGTGGATGCTGATTCAGGGGTTGCGGA
ATGTGTAACTTGTAAAATTTTGATATCCATCGTCTTTATTGGCCTTGGCT
GAGTTGCAGAATAAGGAGGTTTGTGATCTGTATGCTTGCAGAAAAGATTT
TGGAGCAAAGTTTTCTTATATGTGAGATGGAAAACTTTAAAATTTTATGA
TCTTGAATTTCGTTTTTTTCCCCAA
Sequence Length: 
7175
Sequence Checksum: 
7f3a8f0c271d61af8e536dd7ea5f9457
View location in JBrowse: 
DCARv2_Chr1:4140933..4148107-
Gene: 
LOC108204961
Gene Biotype: 
protein_coding
Gbkey: 
Gene