LOC108223044

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108223044
Identifier: 
LOC108223044
Cross Reference: 
NCBI Gene
Relationship: 
There are 4 relationships.
Relationships
The mRNA, XM_017397093.1, is a part of gene, LOC108223044.
The genetic_marker, MK008802 85036.31401, is located in gene, LOC108223044.
The genetic_marker, MK010377 5_34989278, is located in gene, LOC108223044.
The genetic_marker, MK004487 K1931, is located in gene, LOC108223044.
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_017397093.1XM_017397093.1mRNADCARv2_Chr5:34986781..34993834
Sequence: 
CACACAGACTCACTCTCTATATATACACCACTCCACTCTCAAACGACTCA
TCCTATTTTCACTTTCTCTCTCTACAAGCTCAGTTTGTGTTTGAGTAGCC
GACTCTCAATTAGGGTTTTTCGATTTTTTCGGAGGTAACAATTTACGCCT
CTCCGCTCTCAAATCTCTCTATCCCTCTCGTTTACGTCCTTGATTAGCTC
TGTTTGCTTCGTTTAATTCGGTGATTTGTGTGTTTTTTGAGGTTTTGTTT
GTGTTTTTTAGTGATTTTTGTGTGTTTTTTGTGTTTACATGATTTTAGAG
CTTGAATTTGTTGTTTAATTTAATTTATTTGTTTTTGTCGGAGTTATTGT
GTTGATTTTGGTGGACATTTTAGGGCTTTGTGGATGAAGTTGTATTTATA
GGCTTGCTTTGTACACGTGAGCATTTTGATAGTGTAGATCTGTGTGTATA
CATGTTTTGTGTGTGTAGAGGTTAGGGTTTGAAAATTTTGTTCGAGGTTT
TTGTGTCTTAATTGTGTTTATTATGGAATTTCTGTGTGTGTGTTTGTGTT
ATTTGAGGTCTGATGTTTATTGTAATAGTAACATGTGTTTGAAAAATTTG
TTCGAAATTTTTTGGTTCTAATTTTGTTTATTACAGTATATGTTAGGGTT
TGAAAATTTTGTTCGAGATTTATTGTGTTTTACTGTGTTTATTATAGAAT
TTGTGTGTGCGTGTGTTATTTTGAGGTCTGCTGTTTATAGTAACACGTGT
TTGAAAATTCTGTTCGAGATTTGTGTTGTAATTGTGTTTATTATAGAATT
TGTGCGTGTGTTATTTGAAAGTCTGCTGTTTATAGTAACACGTGTTTGAA
AATTCTGTTCAAGATTTTTTTGTTCTAATTGTGTTTATCATAGAATTTGT
GTGTGTTAGTGTTATCTGAGGTCTGATGTTTATTGTAATAGTAACACGTG
TGATTTTGTACATATGATGGATAATATACTTTTAGGTGTTGATTTGTAGC
ATGCATGTGGTTGTTTATTTGATTATATACATGTATGTGTATGAATGATT
CAGGGAATAACACTAGCACTTCTTCTCTTGAACAGTTTTTGAAACTTGTA
CATGCGCTGTTGTCAGTGGATATAGTATGCCATAGTTTTTTAGTTTTTGT
TATCAGACATATATATTGTTTTTTGTGTTTTTGTACCTTGTTTGAAGGTC
TCACTGCTTTTGTTTTTCATGCTTGAGAAAGAAATATATGTGATGATGTG
TAGTTCTTAGAGTCTATAAAAATGATCTGTTATGCTTGTTTATGTTATGT
TCTAATACTCTTTTGAACTTTGATGCTTTCAATTGTACCTGCTATTCATG
GAAATATTTTCTATATTTTGGATGTAGGAAGTGTGATAATGGAAGCATCT
GATGCAGAAGTTAATGGAGCTAATGGTAATGGTGTTAATGGGAATGGTGT
TAACGGGACTAACGGTGTTAACGGGAATGGTAATGGTGCAGTAGAGGAGG
CTTTGCCACCGCCTCCTCCCATACCTGAAGATGTTGTTCCCATTCGTGTA
GTAGAAGATCCTGAGCCGCCTGTGGTGAAGAAGCCTCCACGAGTGCCTAT
TGCGAGGCGTGGCCTTGCATCAAAAGGGAACAAAGTTCAGCTCCTAACTA
ATCACTTCAAAGTGAATGTCACAAATGTTGATGGACACTTTTTCCACTAC
AGTGTGAGTTTCTTCTACCATTGTTTTAAATTGTCAGCTGACTATATATC
ATGGTGTACCTGCTTTGTGTTTTTCCAATTGTGTTGTACTTTCATTCAGC
AAAAAAAATAAAAATAAAAATTGTGTTGTACTTTAACTGTCTTATCCTTG
TGCTTTTGTGAATTATGTTGGGCTGGTATGCATATCTAATCCTGACAACT
TCATTAGGTTGCCCTGTTTTATGAAGATGGACGCCCAGTAGATGGGAAAG
GTATCGGTAGGAAAGTGCTTGATCGTGTGCATGACACTTACAAGGCGGAG
TTGGAAGGGAAGGACTTCGCTTATGATGGGGAAAAGAGCCTGTTCACCGT
TGGATCTCTCCCAAGGAACAAGCTTGAGTTCACTGTTGTGCTTGAGGACA
TGTCCTCTAATAAGTAAAATCCTTCTAATTTTGATTTTACAATTGTTTAC
TGTTGTGCTTGAGAATATCTCATCTAATGTGCCATGTCCTTATAGCATGA
TGATGATGATTGTTGTTATCTTCAGGGTCAAAGGGAATAGCAGTCCTGCT
GCTGATGGAAGCCCCCATGAGAGCGATCGCAAGAGAATGAGGCGCCCATA
CCAATCGAAGACTTACAAGGTGGAGATCTCTTACGCTGCAAAGATCCCAA
TGCAGGCCATTGCACAAGCTTTACGTGGTCAGGAATCTGAGAACTCTCAA
GAAGCCCTAAGGGTTCTGGACATCATCCTCCGACAGCATGCAGCTAAACA
GTATGTTATTGTTCCTGATCATGTTTAGGTTTGTCCTGCATAATTGATTG
GTAACAAGGTGAACTGCAGGGGCTGCCTCCTGGTGCGACAATCATTCTTT
CACAATGATGTGAATAATTTTACTGATGTTGGTGGTGGTGTTCTTGGTTG
TCGTGGATTTCATTCGAGTTTCCGTACCACACAGGGTGGCTTGTCTTTGA
ATATAGGTGCTTCTGTTAGTATATTAGATTATAAATGAATACATGGTTTA
TATTATTTACCTTATCAATACTGGCATGATGTCACCACAGATGACTTATT
TATTTAGTTTTATTTATGACACTCAGATGTATCTACCACGATGATTATTC
AGCCTGGACCAGTTGTTGATTTCTTGATAGCGAACCAGAATGCCAAGGAC
CCATTCACTCTTGACTGGGCAAAGGTAATCTGAGGTTTACCGTCTTCTCT
CTCTTCAGCTATTTGTTTCGAAGTTCTAATATTACCCTCTGTGCAGGCCA
AGCGAGTTCTGAAAAATTTGAGGGTCAAGACAATTCCAACTAACACTGAG
TTCAAGATTACTGGACTTAGCGATAAGAGCTGCAAAGAACTTATGTATAC
TTCCAGTGCTTTCTAATACTCCTTTTATTGTAACAACCTGATGGATATGT
TCCTGGATCCTCTTAGAAACAACTGTTCACCAGTGACCAGTCTCACCTTT
TTGTCATTCCATTTTCAACTTTTTAATTTTACTTGTCTAACTGAATGTTT
TGTGTTTATTTTGGTTCTGTAGGTTTTCGATGAAGCAAAGAGGTGAGACA
GATGAGAACGGGGAGCCGCTGACGACTGAATTATCTGTCTATGATTATTT
TGTGAATGTTAGGAAAATCTCCCTGAAATATTCTGGTGATCTTCCATGCA
TTAACGTAGGAAAACCGAAGCGACCAACATATATCCCCCTGGAGGTGAAT
TTCTTTCTCCTTCATTTTAGTTTGTTCTCAGGTTCTTTATACAATAAGAA
TTACTCTCTGACGTGTGGACTTTTGTTCAACTTTCTGCAGCTTTGTTCCC
TGGTTTCCTTGCAACGGTATACAAAAGCTTTGACCACTCTCCAGAGAGCC
CAGTTGGTGGAAAAATCAAGGCAAAAACCTCAAGATAGGATGAAGACACT
TACCAATGTAATAAAGAACCTTTTGAATCAGACGATTGTGGTGGAATTGT
TTTATTTACTTATATCATGGTGTTTGCAGGCTTTGAGAATCAACAACTAT
GCTGATGAGCCTTTGCTGCGTGCTTGTGGGGTTTCAGTTAGCAATAACTT
TACTCAAGTTGAAGGGCGCATTCTTGCAGCACCAAGGGTACCCACTTTTC
CAGTGCTCTCCCTATATCATTTACTCTACTGATACCTCTCAGCTTAGTTT
TGTGACAGAAGATACTTTATTAGTGAGTTGGTGGTACTTGATGTAGAGAA
TGTGGGGCTTATGTATACATTTTCGAAGTATCCATAAGCTCACATTCTTA
AGTTTCAATGTTACTAATTGTTTTTAGACTTTAATTTTTATACGGAAGTC
TTTATCTTTTACATTATTTTATATGTAGTTGAGGGTGGGTAATGGAGAGG
ACTTCTTTCCTCGTAATGGGCGCTGGAACTTTAACAATAAGGTGTGTATT
ATGAATATTACATACTACTTAAAGATTTTAATAATCTCCATCTTTCTCTA
AAAGATTTTGTATGTGATTGAATAGAAATTGGTGGAGCCCACTACAATAG
ATCGCTGGGCTGTTGTTAACTTCTCTGCTCGCTGCAACATTCAAGGCCTT
ATTACTGATCTTATCAAATGTGGAGGGTTGAAAGGAATTGTATGTATGCT
TCGTTAATTAATAATGTGCTATGTTCAAGTTTGGAATGCTAATGTTTAGT
GTTTTCTCCTATATGTTCTTTTTAATAGAATATCGCTCGCCCTTTTGATG
TGTTTGAGGAGAATCCCCAGCATAGGCGTGCCCCTCCTCTTGTTAGGGTT
GAGAAAATGTTTGAGTCTATGATGTCAAAGCTACCGGGTGCTCCACAGTT
TCTTCTCTGTTTACTTCCAGAGAGGAAAAATTCCCTTCTTTATGGTTTGT
TCCCAGTTAAATAAATTTCCGGGCTCTTATAATTTCACATTTATCATTGA
TAATTCAGTGTTAGCTGATGCAACTCTTCTCTGTTAGGTCCCTGGAAAAG
GAAGAATCTGGCTGAGTATGGAATTGTTACACAGTGCATTGCTCCAACAA
GAGTCAATGACCAGTATTTGACAAATGTGCTTCTTAAGATAAATGCCAAG
GTTATTTTGATATAATCCAAACACTGGTCATTGTGATAATGTGATATTTT
ATTGGGGGTCTGAAGTTTAGGTTTTTAACTAGTTCTTTTCATTGTCCTGG
CAGCTTGGCGGTCTAAATTCGAAGTTGTGCATTGAAAATTCCCCTAGTAT
TCCGTTAGTATCGAAAGTTCCTACAATTATTCTAGGGATGGATGTCTCCC
ATGGATCTCCTGGGCAATCTGATGTTCCATCGATTGCTGCGGTAAAGTCT
CTTCTTAACTAAAATTTTACATTTGGAGGTAACATTTGTAGGAAGGTTAT
ATTGTTTCTGAATTTGACACAGGTTGTTAGTTCAAGGCATTGGCCATTGA
TCTCAAAGTATAGGGCATCAGTTCGAACACAGTCCCCAAAGGTTGAAATG
ATCGATTCTTTGTTTAAAAAGGTTGCTGATGACAAAGATGATGGGATAAT
GAGGTATATGTTCATTTTAGTAGTTCACTAGTTGTTCTATTGATTGAGCA
TCATGAATCTTTATTTGATTGGCAAGCCTGTGGAACTGCAGTTTTAGCTG
TGAATGATCAAGGCTTCTCTGTTTTTGCAGGGAACTTTTGCTGGATTTTT
ACACAAGTTCTGGAAAGAGGAAACCTGATCAAATAATCATATTTAGGTAT
TTTCTGTTCAATATCTTTTTTGTTTGAATAACTGAATCATGAGTTGTCGA
ATTTCTATATGCACTTGGTATTCAGACAACTCACTTGTCGAATTTTTCTG
GAGTGCAATGTCCTTTTATTTGCTCAGTTGTCGAATTTTTCTGGAGTGTA
ATGTACTTCTATTTGCTCAGCAGTAAGAAACTAAGTTGTATGCTTTTTAC
GTATTTCAATACTTCTTTAAGTGTGCACAATTATACTAGTATACAATGTA
TATTTATATGTACAGTACTACAGTAGTAATGTTTTGTTTCTCCCTAAAAA
CATCAGGGATGGTGTCAGTGAGTCTCAGTTTAATCAGGTTCTGAATGTGG
AACTGAACCAAATCATCGAGGTATGTGTGGTGCATGTATGAAATTGTTTC
ATTTGTGTTCCATAATTGTATAGACTTATTTCTATAATATTTACAGGCCT
GCAAGTTCTTGGATGAGAAATGGTGCCCGAAGTTTACTGTTATCATTGCA
CAGAAGAATCATCATACCAAGTTCTTCCAGCCGGCATCTCCGGATAATGT
TCCACCTGGTAGAAATGCTTTAAAATATTGATAACTTCAGAGGCTTATAT
GCCAATAGTTAGCTTATATGATATGCTTTTTTTCTCTCAGGTACTGTGAT
TGACAACAGGATCTGTCATCCGAGAAACAATGATTTCTACCTCTGTGCTC
AGGCTGGAATGATTGTGAGTACTTTAACCTGCTAGTTTTGAATTTATATA
GTCATTTTTCAACTCCCACCAGATTCTCTTAATTTTATGAGATTATGTTT
GCTTGATTGACATTGTGAATTCTATATGTTTGTCTGCTAAATTGAACTTT
TAAAATTATGTTGCTTGATTGACATTGTGGATTCTATATGTGTTTGCCTG
CTAAATTGAACTTCTATCTACGATAGGGCACCACAAGGCCGACCCACTAT
CATGTTCTGTTGGACGAAATTGGTTTTTCCCCTGATGATCTCCAGGAATT
TGTTCATTCTCTTTCTTATGTGTAAGTATTTCTCTCTCTGGTTTTTTGGC
TCTGTTATCTTCTGTGATAGATTTGTAACATTTAAGTTTGCGTGATGATG
TAATTTCAGGTACCAGAGAAGCACAACTGCTATTTCTGTGGGTATGTAAC
TTTTCAACCTGTGCAAATCTTTTCTTGACTTGTATATATTTCCACCTATC
CATTGGTATTTTTCATTCTGGGATTTGATTTCTGTTCTCTCCTTGTTGCA
GTTGCTCCAATATGTTATGCTCACTTGGCAGCTACTCAGATGGGCCAGTT
CATGAAGTTCGATGATATGTCTGAAACGTCTTCAAGCCATGGTGGAGTGA
CTGCTGCTGGACCCGCTCCTGTGGCTCAGTTGCCACGTTTGCAGGAGAAA
GTGTGCAACTCTATGTTCTTCGTCTAAAGACTGCTGAATGTTTGAACTTT
AGATGGTCTTTTTATGTATATATGGTCTCCAGTCTAAACTTCTAGTCAGT
TTGAGCAAGTTGTTAGAATGCTTTTGGACAGCAAGCCTGTATGGCTTTAG
TTTATGCTGCTTCTATTTTGCCAGTATGGAATTTGGATGAGATGCTAAGA
GTTTCTGATCTCGCAGTGTTTTTTGTTAATGTGCATGGTACTTCTAGTTG
AAA
Sequence Length: 
7053
Sequence Checksum: 
2194122b47e02d55cd0b2ec239434364
View location in JBrowse: 
DCARv2_Chr5:34986782..34993834+
Gene: 
LOC108223044
Gene Biotype: 
protein_coding
Gbkey: 
Gene