LOC108213289

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108213289
Identifier: 
LOC108213289
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017385068.1, is a part of gene, LOC108213289.
The genetic_marker, MK009960 3_1520050, is located in gene, LOC108213289.
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_017385068.1XM_017385068.1mRNADCARv2_Chr3:1519670..1526788
Sequence: 
ATCTCTGCCCTTCCACCCCCTCGCACAAAAACACAAAAAACATTAAAAAT
CTCTCTCATCTCTCTCTCTATCTCTCTGCATTCATTAATCTTTAATCCAT
AAAAGCAGATCCTGCATCGTTGGTTTTAATCTCGACGTTAAATCCAATTT
TTTTATTAAAAAAATCTCGAAAAAAAAGTAGGGTTTGAGAAATATGGCGC
AGATTCAGGTGCAGCAGCCGCAGATTCAGGTGACGGGCGGCAATGGGGTG
GCGGCGGTCGTGGCGGTGAACGGCGGAGGGAACCAGTTGTCGACGACGTC
GCTTTATGTGGGTGATTTGGATCATAGTGTGACGGATGGACAGCTGTATG
ATATGTTTGCTCAAGTGGCTTCAGTGGCGTCTGTTAGGGTTTGTAAGGAT
ATCACCACTAATCTTTCGCTTGGATATGGCTATGTGAATTACAATAGTCC
TCAGGATGGTAATCAACTTCACTTTTTGATGATATGTGCATTTTATTGTA
TCGTGTGTCTTGCCATGCGGGTGCGATTGGATAGTCTGAGTGGTGTGAGG
GGGTATGGTTATCGTCGGGTCTTAATTACGCGGGTTATTATTATTAGAAC
ATTTACTAATTTGTGATTGTGACATGCGAGTACAATGTGGATTTTGGGTA
TTATGAATTTATTTATTTCGGGAGTTTTTTTTATGTGTTTATAGTGATTG
TGAATGTGTAATTTAAGTTTACGTAATTGAAATTCTGATATGTTTGATTT
TGAGAAAAAAGTTTGGGGATGATTAACTAACGATGCTTGCTGAAGTGGTA
ATGACTTTAGACATGCGGATTGTGACTGCAAAGATGTTAAGCTGATAAAC
TCTCCTAAGACCTTAAGGCGTAGGGAGTTTCATAAGATCATATGTCATAT
TTGGCAAAACTCTTTTTGAACTACTTCAGATCACTTCATGTCACTTAATA
TTATGTGATGAAGTTATATTTATTTGTTTGTTTAATGAGTAATGCTGGAG
ACCAAATTTGGGTCCCAAAATTTTTTCCCTGATGACGTGGCATATGGACT
ATTTTGATCATCATGATGATGTTGATGTGTATAGAGGGAGTTAGGCTCCA
TCTTATTCAATTGTAACGCATCGAATCAGAGATTATCACGTGAAACTTGG
GATCGTTTTTGGGGTCTCTAGCATTTTACTTGTTTAATTTGTCAAATTAT
ATGTCGTTAATAGTCATCGTTTGTTTTCTGTAGACAACTTTAGTCTACTA
TAAGCGTAGATGCATATCTTTTTTAACATCAGTTCATTCAGCCAAGGAAC
ATTTTTTAATCCGATACATGGTGATTCTACTGCATGACTACTGATGGTTA
ATCACTAATGTTATCATTTTGAACTTTTTTGTGGAACTAACATTTGTCTG
CACTCAATTATTTGATCATAAGTGAATAAAATTGCTAGTTTGTTTGTGCT
TAGAAGACTTATTATGTCATTAATGTATAACTGCTAGTACTTTATGTGGG
AATATAGTTTTTGGAATGTTGTTTATGTACACAGGACACTTCATTGGTGT
AGGTGTAATGTATGTTTGAATAATAGGTGACCTTGAATGCAGTGATTTGT
TTTTAATTTTTGAGAAACGTCTTGACAACAAGCTTCAAATTCATGCAACA
GCCTTACCCTTCATCGTATATCCAGTTTTTTTTGGATTTACCAGTTGGAT
GTATTTACGGTTGTTCAGTCAGCATTTTTAGTACATGTTTTTTAGGTAAT
TTGATAATACTAACACTCTTTTTCTCAATTGTGTACAGCGGCAAGGGCAA
TGGATGTTCTGAACTTTACTCCAGTGAATGGCAAATCAATTCGGGTCATG
TACTCTAATCGTGATCCCACTATTCGGAAGAGTGGAGTAGGAAATATATT
TATCAAGGTACTGATATGATATACAATTACTTAATTTGTAATACTCATCT
GTTTTATATCCTAAGTATTTTGATTGCATCTTTTTTAGCTTAGAGATCTC
ATTCGTCATAGTAAAGGTGATATTGGGAATAATTTTACCTGGTCTGCTCT
GTTTGGTTCCTAGTCATTTTGAGTTGTTTCTATGTGCATATAGGCTTTAT
TCTTTACGCATAACTAGTGAGACATATAACACATTTGTATGCCTATAAAA
TTCACCAAAGTATTCATGTATATGCATATACTATATGGTTCTCTGAGGTG
CTAGTTTTGGAAGTTTATATTCTTGTTTTGAAAACCTTATGTTGTACGTT
TGTGCAGAATCTGGACAAGTCTATCGACAACAAAGCTTTACATGAGACTT
TTTCGAGTTTTGGCACTATCCTTTCTTCTAAGATAGCGACTGATCCATCT
GGGCAGTCTAAAGGTTATGGTTTTGTTCAGTTTGATAGCAAAGAAGCTGC
ACAAAACGCGATAGATAAGCTAGATGGCATGTTGATGAATGATAAACAAG
TTTACGTTGGACATTACATCCGTAAAGAGGACCGAGATGCTGCTTTGAGT
AGGGCAAAGTTCAACAATATATATGTGAAAAATCTTTCCTCAGCTACAAC
TGAAGATGATCTTAAGAAATTATTTGGTGAATTTGGAACAATTACTAGTG
CAGTAGTGATGAGAGACGGGGAGGGTAAATCTAGATGCTTTGGATTTGTC
AACTTTGATAATCCAGATGCTGCTGCTGAGGCTGTTGAGGCCATAAATGG
AAAGAAGTTTGATGATAAGGAGTGGTATGTTGGCAAAGCCCAGAAGAAAT
CTGAAAGATTGATGGAATTAAGAAGTCAGTTTGAGCAAATCGCAAAGGAA
CAATCGGACAAGTTTAAAGGATTGAATCTGTATGTCAAAAATCTTGATGA
CACAATTGATGATGATAAACTGAAGAACTTATTCTCTGAATTTGGAACTA
TCACATCTTGCAAGGTATGTCAATGGACAAATGAATATCTAGAAATGTTG
ACATTTTTTTATCATTGTCTTTGCGCATGATGTATTAATTTTTTTGTTCT
TCATCATATCACGACTCTTTACATTGCCTGTGTTTTCCTTCTCTTCTTTA
TAGGTTATGCGTGATCCCAGGGGAATTAGCCGAGGATCTGGTTTTGTTGC
TTTCTCAACTCCTGAAGAAGCTACTCGAGCTGTGAGTAATTATTTTCTGC
CCATATCATTGATTATTCATCAGAAAATTAATCAGTTTTTTTTTCTGGCG
CAGCTCGCTGAGATGAATGGAAAGATGACAGTGAGCAAACCACTTTATGT
TGCCCTTGCTCAGCGGAAAGAGGAGAGAAGAGCAAGGCTGCAGGTATAGC
TACCATAATTTTTTTTTTTTATCATATCTACTTGCAGAATGAATGTATTT
ATAGTAGTCCACTTTAGTCACAATGGTTATGATAATGACTACATGTTCTT
GTTTCGTATAATTTTGTGGATTGTGCATCTCAATCGACTCGCTCCGAACA
AATTTAGGCATTTTATAGTAGGTCCTTACCCATGCCATGTTTTGTAGTAA
TCTATATATCTAAAAAGATTGGTTCTACTGTTTGTAAATTTGTCACAACT
AATAATGATAGGCTACTTCACTGCCAATTGCACCTGTAGTCCTGTACTTG
TTATTAAATCATCAGTTGTCAGTGTCAGTATTTTCTTTTGCAATTATCAG
TTGTCAGTATGAATACTTTCTTTGTTATCAGCGAGGGAAGTATGTGGAGT
GCTTGATTTTTCTGTATTTGAATAGCATGTTAAATAAATTATATCTGATA
TTTCTGCTCTCCACTGTTCTCGTTCACCAATACTCTCCCCTCCCCAGTGC
TCTTCCTGTCACTTATTTTTTCTTTATTTGACCAAATTTCTCATTGGACT
CTGATACTCGGTAACACTGCTACTACTTTTAAGTTTCATTTCCAAGTTTA
TCATTGTTCTTGATTTTTTTTTGAAAAAAGTTACAACTGGTTCTCTTCCA
TTCCCCTTATCTGCCTCTTGTTGTTTATCACACTCTTCGCTTTCCATTTC
CATATATCACTACATGGCTGTTACGTTGCACTGCTCTTCAGATTGGCATT
CAAATTTCAAAATAAGAAAAAGGCTACTGATTTTGTTTTTTGTCAGTCCG
TACTAAATCTAATTGCTCATTCTGTTCTTTTTGGGCAGCGTATTTCGACT
CCTTGGTGGTTGTTATAATCTCCTTACTTCTAAAAAGAATTAATATGTTT
ACCACAAAGGGTATTATAATCACATGGATTAGATATTGCTATTTTCTTTA
TCCCAACTCTCCAATTACTATTTATACTGAAAAGTTTGCTGTGCATTAAA
CCTTTAGGCTTTATCCCACGAGGTTGGAAAATATATATCTATTCCCACAC
TGGACTGCTGATCCTGCTTTTCTTTATGGTTCGTGTTGTGAAATTTGGCA
GGATAATTGTAGCAGATCAGTACTGGAATATACAAGCCAATTACCTCATA
TGCTATTATTCTAGTCCTACTTTTGTAGTATTTATGTATAAAATTTTGCA
TCAGGTGTACAAAAATAAAGGCATGGTACATGTTAATAGAGGAAGAGGCG
CCGTTTTTTTTTTTTTTTTTTTTTTATTTTNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNTTTTTTTTTTTTTTTTTTTTTAATTTCATGGTAAAAATATTGGAGCC
TCCTGAAAGTTTGCATGCAATTTTGATGACTTGGTGGTGAGATGGGGTGG
GATTGCCTAAATTTCACAAAAAACCCATCAAACACCACGAGTACAGGAAA
TTACATGGTGAACATTTCTGGTGGCTGAAAAAAAAAACTCAAATTGTTGA
ATTCTTTTAAGTTCATGTATCATCAATGTAAGCATTTAAAAGTAGGAGGT
AGAGGTGTATCTGTGGTATATAGATTATTAAGAATGTTCTTGGTTATAGT
AGCAGAACCACAATGATCTATTTCTTTTGTATACTACTAGTTGTCCAATA
TAAGCTATTATCACATGGCTAGTGACGTTATGCGGTTAATTCACCCAAAC
ATTTCTTTCTTGCCAATTATAATAATTTATTTCCTCTGCATCGCATGATC
ATGACTTCTGAAACATGTTTTTAATTATTTGCTTCATTTGCAGGCACAAT
TCTCTCAGATGAGGCCAGTTGCAATGCCACCTGCCGTGGCTCCTCGTATG
CCAATCTATCCACCTGGAGCAGCTGGTTTCGGACAGCAACTCTTTTATGG
GCAAGGCCCTCCTGCCATGTTTCCTTCCCAGGTACCAGTTTTTCACTTAA
CTGGTTTATCCTCTTATGAATGAAGGATATCTCAGTTTAAGAAGTTACAG
TTACATTGTTGGTTTAGTTCCTTCATTTTCTATGCTCCTTTTCTTGTTAC
TATGTGTTGGCCACAAAAAAGTTGAGGTTTGTGTAACCCTATAATTTACT
TCTCTTGATTCATCTAGATACCTAGAACCAGTTGATATTATTGATCAAAT
GAATTTTTGTAATATTACAGAAGTTACCATTTTGATAGTATGTGATATTT
GCAGATTTCCGTAACTTTGTTGAAAATTAAAAAGTTAGTATTAATATTTT
CTGATCCTTGTTTATATGTAACAGAGTTTTGCTGGGAAAAGTTACTTTTT
TTTCTCATAGCCATGTCAATGTTGACAAGGACCATAGAGACCTATATGTG
CCATCAGTATACTAATTAAGTTAATTTAAAATAAGTTTGTATCTGACTTA
AGTGAATCATTAGGTTGAAACCCGTTCAGTATAGGATTACACAGATATTG
TAGCTGTAATGATATTTCTCTTAATCAATATTTGATATTAACCTTTTAGC
AGATGATGAATTCGGATAATAAAAATTTTGACCATTACTTAGGCTAACAC
ATCTATGTTTAAAGCTTAGTCAATATGATATCTATATTTTTAAGTGCAAA
TGATAGTAGTAGATTGTTTTAATCACAAATTTAAATTTTGTAGGCTGGGT
TTGGCTATCAGCAGCAGATGGTGCCGGGAATGAGGCCAGGTGGTGCTCCT
ATGCCAAATTTCTACATGCCTATGGTCCCTCAGGGACAGAGGCCTGCTGG
AAGGCGAGGAGCGGGTCCTATACAACAGACTCAGCAGCCTGTTCCTTTAA
TGCAGCCGCAGGTTAAGTAACTGTACATTCTAGTTATTTTGCTTGTATTT
AGTAAAATGTCTGTTTAATAGCATGTATAAAGGTTGAAAACATTTTCTTC
AGATGATGCCAAGGGGGCGCATGTATCGTTTTCCACCAGGTCGCAATGTT
ACAGATGTGACCATGCCAGGTGTTGGTGGAGGAGTGCTCCCTATTCCTTA
TGAGATTGGTGGCGCACTTCCTCGAGAAGCTGTAACTTATCCTATGCCAA
TTACAGCATTGGCTTCTGCCCTAGCAAATGCACCTGCTGATCAGCAGAGA
ACTGTAAGCCTTTCAACATCATGTAAAATGTCGTTGTGATATGCTTGATC
TGTGAACTGACACGACTGTCCTTTTTGGTGCCAGATGTTAGGTGAAAATC
TTTACCCGCTAGTGGATCAGCTGGAGCATGATCATGCAGCTAAGGTCACA
GGCATGCTCCTGGAAATGGACCAAACTGAAGTTTTGCACTTGCTCGAGTC
ACCTGATGCACTAAAGGCTAAAGTTGCGGAGGCAATGGAGGTTTTGAAGA
ACGTGTCACAAGCTGCTACGCCAGCTGATCAGCTGGCTAACCTTTCACTC
AATGAAAATCTCGCCTCTTAAGTTAAGGGCTGTTTCAGTTGTGGTGGTGT
TCTGGATCACCATATCGCGATGTAGTCAAGAAACTAGGTATCTATCATGA
GTCAGTTAGTTAAATATGAAGGGTTGGGAACCAAGTCCTTTTTTTTCTAG
TTGTCATAAGATTTTTCTCTATAATAAGTATTCTGTTAGGTATGAAATTG
AGAACTTAAAATATTTCCGGGTCTTGAATTTGGTAAGAATTTTTCGGCTA
TAGTTTTGATAATAATAT
Sequence Length: 
7118
Sequence Checksum: 
56a839d7a187986b6aa081204d55bb34
View location in JBrowse: 
DCARv2_Chr3:1519671..1526788-
Gene: 
LOC108213289
Gene Biotype: 
protein_coding
Gbkey: 
Gene