LOC108192882

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108192882
Identifier: 
LOC108192882
Cross Reference: 
NCBI Gene
Relationship: 
There are 4 relationships.
Relationships
The mRNA, XM_017359404.1, is a part of gene, LOC108192882.
The genetic_marker, MK009668 6_22511995, is located in gene, LOC108192882.
The transcript, XR_001801072.1, is a part of gene, LOC108192882.
The transcript, XR_001801073.1, is a part of gene, LOC108192882.
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_017359404.1XM_017359404.1mRNADCARv2_Chr6:22507655..22514166
Sequence: 
TCTGAAACGCCACTAAAAAAGAAAAAGAAACATATTTTTTTGAAGAAGAA
GCATCTTAACATTTTTACAATTCAACATCAAAAAAAAATTATATTCCTCA
CATTGATCATCCTCAGCTCTGGTAAATCCTTAGCTCTGTATCTATAATTA
ATCTTTATATTAACTTTGTGCATTTTTTTCATTTGTTGATTTACTGTTTA
TTTTAATTATTGCTGAGCTCAATGATTTGTTACTTTGAAGTTTGACCTGT
TGCTAATTTTGCTCGGTGATCTTGTTTATATATGTATCTATAGTTGTCTG
TATAGTTGTGTGTATATTGGATCTGTATTTGATCACTTGCATTAGTTGCT
GATTGTTATGAACTTCATTGTAAATTAAGCTGTGATCTGAATAGATTTGT
CATCAGATTTTAGTTGAAGTTAGTCTTTACTTATTTAGGTTTTAATTTTA
GTTAAATAGTAGTAAGAAATGCAGTATACATTAAGGGGACGTTTGATAAC
AGGTTGGAATGGGTATCGGGAATGAGAATGAGGGGATGGGAATGGAGGGT
ATGAGAATTGGTATGTCAAGGGGAGTTGAAGGAATGATTTACCCACCAAG
TGGGAATGAGGTTCCCATTCCATATAACAAAATTGCAAACCTAAACACCA
ACACATGGGTTTGAGGTTCCGGTTCCCGTTAACCGGGCTCATTAACCATG
AACCAAAAGCCACCTGAGTTGATGGTAATTGTTTCAGTTATTGTTAGTAG
TTGAGGGGATGGAGGCGGAATCAGGGACTAACAAGCTCAATTGCACTTTG
AACTGACAAGACAAAGTTTTTGTTTTGTTTTTATGATATTGAACCTATGT
GTTTGCTTCGTTTCCCCCTTTTAGCTCTGTGTTATGTGCGAGTGAATTTT
TAATCTAGTATAGTGACTGACATGTGAGTAAATTAAGCTGACTAGATTTG
ACTCTTTTTGAAGTGTAGTTCTATTTGTGCTTTAGGTTTTCTTTTGTGGA
ATTGGGTTAGACAAGAGGGTGACCTAGGTTGGGTCATGGATGTGCTTCAA
ATAGTTATTAGTATTGTTTTGGTTTTTGACCTATGTTGTCCTTCTGCATG
GTGATTCCCGCCAATTGTTGTGAACTTGTGATACTTGATCCTAGATCAGA
ATGTGGGTTTGATTAGTGCTATACAAATGTAATCTAGCTCTGGATGATCG
ATTGAACTACTTGCCTCAAATGTGATTCGATTATTGGTCATAGTCTGTAG
GACTTCCATGTATCTGATTAAAGGCCAATTTGGAAATGCTATATCAATGC
ATTCGATGCTTACAGTTCAAACTTTCTACTTTGGCCTTTATTAGAAAAAT
AAAGTTAGTTGAATTTGATCTAGAGTCCAGATATTGGGACTACACCGATG
CTACCTTACAACAGTTACAAGACAATACATTCTCACTTGTGAAATTTTCT
TGTGTTTAGGTCTTTATGTTAAGCCAACTAAATAACATGTATATGTGTGA
TTGATGCTTTCTTTGAGGAACATAGTGACAAATCTGCCTTGCATATAACA
CCTTAATATATCATGGTCCCATTTGCAACAACATTGCATATTTTTGAAAA
CCAATAGAGGCTGCGCCTGTCTGAAATTATAGCCTAAAAGCTAAAATCTA
GGTAAAAACTCCACTAATGCACCAAAGTTTATAAGTTAAAAGTATTTGAG
AAGCTCTTAGCCTCTGATTCCCAGTTATCTGTTCAAAAATAATTTAGTTA
GATAATTGAAAAACCATCTCGACTATAAATTCAAACTTGGTACAAATTTT
GCTTCTTGTTATCTTAGCGTTTGGAACCAAATAAATTAATATATAGCTTG
GCAAAAAAATTTATGATAGTTTTATCACCAAAATTCAATCCAACTTGTAC
GTTTATGACATAGATCGAATTTCATCATATTTTTTTTTGCATGGAATACC
TATGTGGTCGTGTTACCTATTCCTCTATAAAATTTGCTAAATTTTGCGTT
TTCTTTATTATATTTTGCTTTGACTTGTTAAAATTTAAACTTTGTATCTT
AAAGTTTAAACATGTATACAAATTTATCAATCTTAAATATAATACTAATT
ACTCTCTATTTATAATTAGCAGCTATGACATGATATAATCTCCACTTGCT
ATTCCTTAGGTCATGAGTCTTCACCAGGAACTGCAATGTGGGAGCAGCAG
TTAAAATCAAAATGATATTATTACCAACTTTATTCTAGTTTTGTAACAAG
TTGCATGAAGTTTCAGTCTTAATTGATTATGGTCGTAAAATTTTAAAAGC
TACCTGTTTTTTACAAATGCTGGCTATTACTTCTTTTAGAGTCTATAATA
TCTTATCTGCTGTTTGATGCTAATTTTATTCCATTTGGATTATAGTTAAC
AGTTCCAGATTCTAAAAACGATGGAATTTCCTTTCCAATCTTTTCTTTTT
TCTCATTGTTTGTAGTTAGTGAAAGTGATAGTCATATCTGCTAGAGGGGG
TTCTTTGAAGGAGCTTTGGGTGCCATTTCAAGGAGCTTTGCTTTTTCCAG
AGGAATGGTACGGCATTTAACATTTTAAACAACTTAGTGTCCTTTTTTTT
TTTTTTGCTGAATAGGCTATTGTTTGTGCTTCTTTTCCTGACATTTTCCT
TTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTG
CTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTT
TCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTC
GTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTT
TTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAA
TAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTT
TTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTG
ACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCT
TTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTT
TTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTT
TCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTT
TGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTT
TTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTT
CTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCT
TCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTC
TGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGT
TTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTT
CCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATA
GGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTT
CTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGAC
ATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTT
TTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTT
TTTTTTTTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTC
CTTTCTTCGTTTTTTTCTTTTTTTTTTTTTTCTGAATAGGCTTTTTTTTG
TGCTTCTTTTCCTGACATTTTCCTTTCTTCGTTTTTTTCTTTTTTTTTTT
TTTCTGAATAGGCTTTTTTTTGTGCTTCTTTTCCTGACATTTTCCTTTCT
TCGTTTTTTTCTTTTTTTTTTTTTTGCTGAATAGGCTATTGTTTGTGCTT
CTTTTCCTGACATTTTCCTTTCTTCGTTTTCTTCTTCTTTTTTTTCCCTA
CTAATTCTTATTTTATGCCCAATTAAGTGAATACATGACATGACATTTTA
CTTCGTGAGATTATTTCAGAATGACGGGCTGACCTCGTATATAGGGCTTT
TATACTTTTTAAGGCATAGTTTAAACCTAGCTACTGCTCTCTCTGCTGGT
GTAATCAGTTCACCGATGATTATGAATAGGTAGCCCGGTCTCCAGTTCTG
TTATTGGCTCTAGTTCATGCATTGGACCGAGCGACCACGGACAGACCACG
CTATATATAGGTTTTTACATCTACTAAAAATGTAAGAATATAGAGTAACA
CAAGTAGTTTACTAATTATTCAATTACTGATAATTAGATAATTGTCGAAA
GATGTCAAATAGAGTTATCAAATTATGTGATATTTAACTCGTAAGAAATT
AATGATTTAAAATTTTATTGTATTAGCAACAGGGATAATGTAATATAATA
TTTTTATATAAAAATTGTAAAAAATTATACTTCATAATATAAGAATATCA
TCAGAATGTAATGTATACACCATCAAGGGCTCTGGTGTATCCAGGTTGTT
AGCTCAAGGGGTTTCGAAAACTATGTTTGTTCCCTTTCTCTTTTCGCCAA
CCTTCATCACCCAGGCTAGAGCCCTTGGAAATTCGGAAGTATGCTTCAAA
GTAATGATGACAGTACTTATAATGTCTGTGGATAATGTTGATGTACTTCT
GTAATTTAGTTAGGCGAAAAAACTGAAATTACTAAATCAGGTTACAAATT
TTGTTTACTACTAATTACAATACAAAAGATAATCTTAATTTTTTCAGCAA
AGAATTTTAGTTGGTTTTCTTGGGGTTGAGAGTGGGGTTCGGGAGATGGG
CAAAAAAAATTCAAAATTTGTGGAGGCAACAGTAGTGTAACTCAGATTTT
CAGCATTACATTTTTGGGGAATTAAGCACTGATTTGGCAATTTCAGCTTA
GCCAAACAGGTATGCATTTAAAAAAGTGAACGCCTCAACTCAGAAGATGT
TTTTAGTTTTATGTGAAGTTATATAAATATTTATCGAAGTTGTCTGGCGC
AGGGCTGATGACTATTGTGTAGTTAGAATTTTCTTGCAAGTCTGCCCACA
CTTGGTTACTTATGAACTTGTTATCTCCTTGAACTTCAAAAGGCTCTGTT
CCAGTAATAAAGAAATAAAAACACCTTGCCCGCAAATTAGTTTATAATTT
ACTCCTGGAAGTTAATGTAGCTGATTTGTGCATGTATAAAGGAACACAAT
CACTTAACAATAAAGACTTTCATGGCCATCATGGCTGAGAGGGATGCTGC
CATTCGAGAGCGGAACATGGCTCTGGAGGAAAGGAAAAGGGCCTTTGCTG
AGCGTGATATGGCAATGTTGCAGCGAGATGCAGCACTTCAAGAGCGTGAT
TCTGCTATGAGAGAACGAGACGAGGCAATGGCTACACTACGGTACAAAGG
GGGAAGTTCAGTGAACGAGAATAATACGAGTTCTGACTTTCCCAATAATG
GGGTAGGACGTGGAACAAAAAGCATTCAAGAAGACCAGCAAATGCATATA
ATGTATGATATGTCTTCTGGAAAATATAGCCCAGGAGATATCATGACAGA
TTCCTATCAGATTAATGATGTTCCTACTGAACATGTTAAACCAAGGAAGG
TTAAGCAAACAGAAGAGAATAAAGAATTTCCTAAAAAGCCAGCGAAGTCA
CGGAGGGTGAGTAGAAAAGGAGCTGAAAATCTGAAAAAAGAGGGATCCGC
ATCTGCATCAAATATTTGCAAAATTGAGCAGGATTTGGGTGCGGATGAGA
ACCAAGGTAGTCAGATTGCTGGTTGGAAAGATAGTTTAGAACTAAATCAG
GTAAATTTTGATGATTCTGCCATGCCGATTCCCGTATGCTCCTGCACAGG
AGTACCCCAACCATGCTATAAGTGGGGGAATGGTGGGTGGCAGTCTGCCT
GTTGCACAACTACAATGTCCATGTACCCTTTACCTCAAGTATCAAACAAG
CGATATTCTCGTGTTGGGGGGAGGAAGATGAGCGGAGGTGCTTTCAGCAA
ATTACTAACTCGATTGCATGATGAAGGTTATGACCTATCGAGTCCTCTTG
ATTTAAAGGACCACTGGGCAAAACATGGCACCAATCGCTACAGCACTGTA
AAATAGCTTGCAACTCTATGCAAAGATTGGAGACATAAGCTATGGCACTG
AGTTTATTCTGAAGTGGATATCTGGTGTTTTGGATGGGTATCGAGATCAA
ACACATTTTAGAGACCAGATGGTTCACAGCTTACTTGGTATTTTTCCTAC
CTGCAAATCCTGCAATTATATTTCCTTATTTTTTATTTATATCTTTCTTA
TAGGAATTTGATTGAGCAGAACTTTGATCTATGGCTGACAGCCAAACAAA
AAGATGTTGTACCAGCTTTTGAATGATTGTAATGGAATAGAAACAACAGG
ATCGTATGCTATATTCTTGTATTGTTTTACATTTTTATTTCCTTTTTTCT
TGCAGCAGCTAGAGGTTATACTGTTGATACCAATCTCACTCGCTTAAGAG
AACAACTATAAAATAGGGGCCCAGAATACTGGGAGTGAGAAGCTCAAACT
CGAGAACTCTTCTAAATCTGAGTTCACATACAATAATATTACTGTGTATT
ATTGACTTCCTCCCATGGCAGATGTTGGACACGTCCTCAATCAGGCACAC
ACATGTCCAAAGGCCAGCATAATTAACGGACGGTCCCAATCATTGGCCTA
TAATGGTTGGGGCAATGGGGTTGTTGTTGGGCCACAGCCCAATAAGGAAA
AGCCAAGCCAATTAAGAGGCCCAGAATGCAAACTATAGCCCAGCTGATCC
GAAAACAAACGGAATTCACATAATCCTTTCTTTAGTTGTGAGCTTGCAGT
GCGAGCTTGAGCCTCGTCGTCTTTTTGATGATGACGCAGATCTAGACATG
GAGGAGCAACCAACTTGTTCAGATCCGGTTGGAGGTCACCGATGCCGAGC
TTCAAAAATGATGGCGACAAAGCCGCAGGGGAAAAGAGTTCTGACGAGTG
ATGCTAGGCTTCATTTGGAGGATGAGGTTAAGTCTCTTGACAACGAACGC
CGTCTCCTCGTGGCGAAATTGAGGCAAAAATGAGTAACAACACATCTAAA
AGCTGAACTGATGGTCAATTAGAATGAAACCGACCATCTGTGTATCAAAC
TGAGGATTATAAACTTTTTTGGAGGACTTCTA
Sequence Length: 
7282
Sequence Checksum: 
3fa4f440c82b1132492339f28a15a50e
View location in JBrowse: 
DCARv2_Chr6:22506885..22514166-
Gene: 
LOC108192882
Gene Biotype: 
protein_coding
Gbkey: 
Gene