LOC108202676

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108202676
Identifier: 
LOC108202676
Cross Reference: 
NCBI Gene
Relationship: 
There are 4 relationships.
Relationships
The ncRNA, XR_001803197.1, is a part of gene, LOC108202676.
The genetic_marker, MK003912 K1356, is located in gene, LOC108202676.
The ncRNA, XR_001803196.1, is a part of gene, LOC108202676.
The ncRNA, XR_001803198.1, is a part of gene, LOC108202676.
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.
Sequence: 
TAGAGTATCTCCAGGAGCCTCCTTATTGGCTCCTATCTCTTGGAGCAACA
TTTTTCCTCTCCCTCCTCAAATCTCAAGTCAAGAGCCTAAATAAATAAAG
AAACTCTTCGAGATGATCTTATCACAAGACCTAGAGCACCCTTGAACCTG
ACAAGGAAAGGAATAGGACAGGTGATAAGGATTCTCAGCCGCCACTTGAT
TGAAATCCAATGGCTTGTATCCTGGTTTCATAAAGTCCCGAGTCGTCTAT
AAAGACTTTCACAGCTGAGGGTGTTTCCAGGAAAGTAACGACTTGATATT
ATTATTAGGTGCTGCTCAAAGAAGAAGAAGCAGAAGATCAGTTATGAAAG
GAAATAAAACATCGGATCTCAATAAAGGTTATGCAAGAAAACACGGTGAC
TCTGAACAAAGGTTCAACTACTTTGCTCTTAGAGTTTTTCATCTATGTTT
ATGTTACTTGATCTATTTTATGTATAATTTTTTCATATATTTCACATTTT
TATTTTTTGCAGATCACTAACAATTTCTTATATTTAATCAGTTTAATTTT
TTATTTATGTTTGTCAAACATGTTAAGCATATCATCATATATGATATACT
CTTAAATCCTGAATCCTTTAATTTTAATCTTAAAAATTATGTCCGCTAGT
GGCTCCATCTCTGATAGCCTCGAAAAACTCGGAGTCTGAATTGATGAATA
TTTTCTTGCCGAGTCGGAATGGGTGATTATTTGGCTGTGTTCGGTTTCTG
CTAAAAATAATGAATATGATGCACTACGCTTTAGATAAAGAACAACTGCT
TAACACCTTGCTGTTGGTATGCCGCATATACTTGGACAATATGTACGCAG
AAAATGGAAGGACATATCTGGCCTAGTGAATGAAAGATATTGTAATTCTT
TGATACGCAGTCTCATCTACTCTAGGGCTGTTCCGGTTTTGGTAAAGAGG
AATGGAAGCGATAGGTTTGTTGGCAACATTACAATCCTTTGCATTTGTGA
TTGAATAATAACATTAGGCTTTTGCGACATTTGAAACTGAATTATTCAAG
TGGACCATGGTCTTCTGAAGAAACAACCTAGCAGAGAGACGAGAACTGGT
GGTGTTCAAATTGTTTACCTAAGCAAGGACATTACCTGTAAATTGGGACT
TGTGCAAGATAAAGAGTGACGTATCTGATTACTGGACCAGGAGGTGGGTA
CTGATCGGAACATAGTTGGTGCCAGAATATTGGTAGGAGTGGCCGTTTTG
AGCATAACTTGGGTGAACTGGAATTATGTGTCGATTTAACTTTGGTACAC
TTAATAATATGCATAAAGTTCTAAAGTAGTCTACATCTGTCTGTGTTTGT
GTTACATGAAGTCATGAACTGAGTTTTCTGTATATTTTTTAATTTCTAAT
ATGAGGATTATTTTTTCTCTGTTTTAATTACATAATAGGTCTTGCTGAAT
ACAGATCTCACAAACTCTATTGAGTCTTTTTCATCAGTGCTAACTGATTT
TCTTTCTTGGTTTCTTTTTCTACTGATATTTCTCATGTGATGTTTTTGTT
GCATTTATCATCCTCGTAAGCTAGAACGACTTCCATTTTTGTTCAACCCC
TCTCCCCCGACCCTTTTTGTTCTATTTGCTGAACCCACCCTTTTTGTTTT
TCAACTGCACTATTTTAAAAAATTTCACAATTCATATTTGCAGTAGATTG
TAAACTACTATATATATTATTGTGATCTATCAAATTATGGTTCGTAGATT
TAGAACACATCTTCTCATATTATGAGTTTATATTCATAGTTGTCACACTA
TTTTTAGATTACTGTTTTCTTGTCAGTGGTTCGTGCTTAAAATAATCAGT
GTGATGCACTATGCTTCAGATAACACGACTGCCTGACAGCTTGCTAGTGG
AACGGTGCATAAAATTTGGACAGTTTGTTCACTGAGGAGGGAGGAAGTAT
CTGGCTAAATGAAAGATGGTGCGACTTGTTCAGTACGCCTTCATACACAG
TCTCATCTAACTCTAGGGCTGTTCAAGTCTTAGTAAAGAGAAGTGGGAGC
CATGGGTGTGTTGGCACTTGGCACCATTACTATCCTTAACTTCAGAGCCA
TTCATTCAGTATTTTCGTGACATAAGAATAGCGGTAGGTTTCTTCTACAT
CTGAACACCTTAAAATAATCAAGTGAACCAAGGTCTTCTAAAGAAAACCT
GGCAGAGACAAGAACTGGTGATGTTGAAGTCTTTTACATCAACATGGACA
TAAAACTTATATTGGGGAGTTTGCAAGATATAGAGTGACACATCTGATTA
CTGGACTAGGTGTGTAGTGATTGGAACATATCCGGTGTCGAGATTTTGGG
TTGGGCAGGGGTGGCTATTTTAGCAGAACTTGGATGAAAATAAAATCAAA
TGTGGGTGAGACTGAATGAGAATTGCAAATGATTGAAGCCTGGGAACGGG
AAAAACTGATATGGTGTTTTATATATAATTAGCTTCAAGAACAGTTGATA
TTTTACTATGGAAGACGATAGAACTGGCATAATACTTGATTTCATAGTTC
AAGACATGATATTAACATCTTTACATAATATATACATAAAGTTATAAGAT
ATGGACATATCTGATGTGATGTGTTTTGTCCTTGAGGCTTATCATTTTGT
TGCTGCTGCTATATTCAAAGATTATATTTTCTTCTCTTATTTTATTACAA
CAAAGTCTTCCTCATACAAATCTTGCAAACTTTCTGGAGTTCTTTCGTCA
CTGTTGGATCTTCCCCAATCTTGTGGGTTGTTTTTGTTTTGCCCATGTTG
TCACGTCGATAAGTCGAGTCGAGTCGATAGAGGTCCAGCTTATCGACTAG
TCGACTAGTCGTAGACTAGTCGCTGACTAGTCGAAAAGTTAATTAATAGT
TAATTAAATAATATATATTATTATATACATTATATACGTCGTTTCCTATA
ACTAGTCATATGTATATCAATCACAAAATAGATATGTTAGTTACAAACAT
ATCTTTTCCCCCTTTTCATGTATACACATTAACACACTACACACATTAAC
TGTACCAATATATAAACAGATTATACTACATGTATATTCAGTTTTAATCA
ACTTATGCATACATAAACACATCCACACACAAAGATCTATAAACTTAGAT
TATCATGTTGATTATTGTTGATTTTGAGTAGTTTCATAGAATTTTATTTT
TTTTTCATTTTAATTTTTGATTGAATTTTACACTTGTCGACCGACTAGTC
GACCAAGTCGACCGACTAGTCGATAAGTCGATCAATTAGTCGACCAAGTC
GACCGACTAGTCGACAATTCGCAAGTCGACCTCTCCAGTCGATTTTCTAA
ACCCGACTAGTCGACTAGTCGTCGACTAGTCGCGACTAGTCGAGCGCCGT
GACAACAATGATTGCTATAGAACTTTCAAATACTGTTGCATAAGAGACAA
GGTTAGTATTTTAACTTTCAAAAGTCCAGCTACGAGCCTGCGATTTTTGC
AACTTCTGGTTCATAAAAAAACGTATGTGGGCCCTCCACTGTCACCTCTA
TACAGGGTTAGGGTGAAGCAAATTAGGCCAGCCCTTGACATAGGGCCTAA
ATCCAGTCGATTAGCACTCTGACAAGTGAAATACTCCAGCTGATCTTAAA
CCATTAAAGGTAAACTATGTTAAAAATTAGCTTACTTGCCAATTGCAATA
ACCAGTACTATAATCTTAATCCATGTANNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGCCTGT
CTTCTTGTAATAGGATATGACACGGCTGTGTTGGTGGGCGTATACAAATA
AACTTACTCTCCATGGTTGTCACGTCGATAAGTCGAGTCGAGTCGATAGA
GGTCCAGCTTATCGACTAGTCGACTAGTCGTAGACTAGTCGCTGACTAGT
CGAAAAGTTAATTAATAGTTAATTAAATAATATATATTATTATATACATT
ATATACGTCGTTTCCTATAACTAGTCATATGTATATCAATCACAAAATAG
ATATGTTAGTTACAAACATATCTTTTCCCCCTTTTCATGTATACACATTA
ACACACTACACACATTAACTGTACCAATATATAAACAGATTATACTACAT
GTATATTCAGTTTTAATCAACTTATGCATACATAAACACATCCACACACA
AAGATCTATAAACTTAGATTATCATGTTGATTATTGTTGATTTTGAGTAG
TTTCATAGAATTTTATTTTTTTTTCATTTTAATTTTTGATTGAATTTTAC
ACTTGTCGACCGACTAGTCGACCAAGTCGACCGACTAGTCGATAAGTCGA
TCAATTAGTCGACCAAGTCGACCGACTAGTCGACAATTCGCAAGTCGACC
TCTCCAGTCGATTTTCTAAACCCGACTAGTCGACTAGTCGTCGACTAGTC
GCGACTAGTCGAGCGCCGTGACAACAAACTTTTGCCTCATTTCTCCTCGT
AAACAGAGTTCCCCTAATTTGAGTTGGAATTAATGAATAATTTATTGTCT
TCCTTCGTGCCAAAAAAACTGTAAATTATGCAGTATGCTTTAGATAACTC
AACAATTGCTTAAGAGCGGTGAGACTGATTGGAATAGCAAAAAAATATAT
ATATATATATATCTAACTTTAGTATGCTGTTATAATCTCTCCCCTAATTT
ATCCACCTCTTTTACATTGTGTAGGCCTGTTTTGTTATGGAGTAAGAACT
GGATAATTGGCAGGTGGATTGCATTGTGCTTTTTAATCTTCTTTTTACTG
GTCGTTGATGTGCACTGTTTTTATCTTCTACGTAAATACAACCCAGAAGA
CACAGTTTACGGTCTGTTAGTTATGATCTTTGGAAACCTGGTCGGCTTTG
GTTTTCTGGGCACGCAAGCTAGAGAACTTATTGAAGATTCAAATACTGTA
AATGATCTGCCTTGGTGGTGCTATGGGTTGACAAGCTCTACATCGGATTG
AGGATTCAATGTTAGGTGAGCTCGAGTTCGACCTGAATTGAAGCTGCAGT
AAGGTTGTAATATCAGTTAAAGTCGCACGGGATGAAATCTAAGTGCTACA
AATAATGTTTCATAGAGGCCTCCAAGGTTCGTCACCCGTGACGTGTTTAA
AAATGAAGGTAATCTGGTTAATTTGTTTGGAAATATAGTAGCCTTTGTTA
ATGGTGACTCTTTCCTATGAATATGTATTGTTGGGCTTTGAACTTCTTGT
TGAAGTTCCATTACTTTTGCCTTTTGGTGTGGTAATTGTTAAATACTTTG
TACTTGTGTTCTGTTAACAGATTTATACTACCCGCTGTTATGAATTTCTT
TTACAA
Sequence Length: 
5656
Sequence Checksum: 
e37d714491222a18873b59a25677afac
View location in JBrowse: 
DCARv2_Chr9:2165138..2170793+
Gene: 
LOC108202676
Gene Biotype: 
lncRNA
Gbkey: 
Gene