LOC108193292

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108193292
Identifier: 
LOC108193292
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017359894.1, is a part of gene, LOC108193292.
The genetic_marker, MK003172 K0616, is located in gene, LOC108193292.
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_017359894.1XM_017359894.1mRNADCARv2_Chr7:31379969..31388560
Sequence: 
GGCATTTATAATTTACACTGTCCCTTGTCTGCACAAACTCTGATTTTTTT
CTCAATTAACCAGGCGCAAAACTGAAAACCCTAGCCTATAATTTCTCCAT
TTCTCCTTTCAATCATGGCTGACTCATTTGAGGAAATAGCCTCATTGCCT
CAGCCTTCTAATATCCACCAGCTTTACGCCGAGCCGCCAGCTCAGAATCC
GGCTCCGGCAGAGCCGGCTCAAGCTCAGCCTCCAGTGGCGCCGCCTCAGC
CTCCAGCTCCATCCAAGCCTGGTAATCAATCAATTATTAAAATTGCACGC
AATTCTCAATTACTGTTGTTTATTAATTAATTAATTAATTAATTGCATGT
AATTCTCACTTGCTGCTTATTTAATTTGTTTGTTATATCTACAAAACTAT
ACAAAATGTTGTATACGTGTGTGTATAATGGAATTGCGGTTTCGATTTTG
AATTTGTGAGGATTATTAGGTTAGTTGTGTGGATTTGGAGGTGGCTTAAT
TAATTTTTAATTTTGTTTGGTTCCTCAAGAATGCAAGTACAAGAATTATT
TGCAAGAATACACTCAGAGGGAAGGCCTCCTTCTACCGTCGTATCATACT
GTTTGGGATGGGGCATCACACTCCCCGATGTTTCGGTCCACAGTGGTGGT
TAACGGTGTAACTTACTCATCACCCAATGTCTTTCCGACTAGGAAAGCTG
CTGAGATGGATGTTGCTGGCATAGCCTTGCGTGGTTTGCTACAACTACAA
CAGGCGGAAGACTGTTCGATAGATAAAGAGGTATTGCATGGAAAATCACT
TGGCTTTAATTTGTTTCTATTTATTATTGATATTCACTGGGTTTGATGTG
GACTTTTTTTATATAGTCTAGGTTATTACGCCTTCATTTGATTTAATTGA
ATGAACTTCTTTAGACGAGAATGTGTGATGGAAAGTTATCAAATTGGTGC
CTAGTTATGATAATGATGCTTGACAAATATGAGTCCATTACCATTTTAGT
TTATAATTATAATGTGATGTGTTTTGTATACACTTAAGGCAATAGTATCT
AATTTTTCCTTTTAAATTCTCGGTGTTGATGTCTTAGTCATATGTTACCA
ACTTATTGGTATAAGAAGTGAGCAAGTTGCACATTATTATGGTCCCGTTT
GGAAGTTAGAGGGTTAAGAAAATATTAGAGGTTTGACTACCGATTTGGGA
TTTTAGGGATCCGTTAATTGCTAAACAAGGCCTATATTTATGAGGAACAA
CTAACAAGACTATTATATACTCTATATAGTAGTCAACAAAAGTAGACCCC
GAGTAAACTACCATAACATTAACATTACACACACACACATACATTTCATG
CTCAACTTGCCAAACCTTCTAATAAGAGGATGAAACATTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTATAAAGGGTNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNTTCCGTTGAATAACTACCAGTGTTATGA
AAAGCGCAAATCGGCTCTAGGCGGTAGGAGGACCTTTTAGCGCTTAAGCG
GTAAAGCGGACGCTTAAGCGGAATTTTAAGCGGGTCAATAAGCGGATTAA
TTAAATATTTAATTATAATATTAATATATTTAAAAATAATATTATGTTGT
GTTAAGAATATGCATTTTTAATATTTTTGATAATTTTTTTTTTAATTTTA
TAATGTAATTATAGTTATATTATTAAAAAATTAATATTTCAAAATTATTT
TTTTAAAAAAAATTAGCAAGTCAACATCATTTTGACCGCTTAATCCGCTT
AACAACCGCTTAATCCGCTTAATTTTCAAAAACGCTTAATCTCCTGCTTA
GTACAAAATCGAAGCGCTTTAGGGGCGATTCCGCTTAAGCGGCCGCTTAA
TGCGCTTTTTACAACACTGCTTACGATAAGTATGTTAAGTTGTTAACCCA
TGGAGGCACAAAGAAACATTTTAGCAGATTAATATACAATTGGAGATCTT
TTCATCTGTTAATTATGCAAATTAAACATAATTATTGCCACAAGCAACTT
TAGGGACATAGAGAAGCCAAAACCTACTCATAATCATTATATGCATTACA
GTATTAGTATCATTATACTCAAATTATCTATACAGATTGCAGCATTTGGA
GTACTTGAGAGTTGCATTTGCATGTAATTAATAATGAATAATGTAATGAA
ACCATGGACCGATATCAAGGTATTGGATCTTTTTGCATGCACATACCATG
TCAGTTTGGTACTATCCGACTTTTATCAAACATCTTACTATTAATGTTTA
ATTGAATGACTAATGGAAGTAGTACTTTTCAACATATTAGTGATCTGAAT
TTATCTGCTGTGAAACCTTCATCTGATAGAATTATAAGTTATATAATTCT
AGAACTTCTACTATACTTTTTTTTTCTTTTTCTTACTTTCTTTGTTTGCC
AGGAGCTCACCCTTTGCAAAGCAATCCTGAAAGAGTATGCAGACAAGATA
AATGTAGGCAACCCTATTTACAAAACAGAACAAGGAGACGGGTCATCAGC
ATTTACTTCTTCTTTAACATTTAATGGCAAGGAATATGTTGGAGAAGCAG
GCCGCAACAAAAAGGAGTCTCAACACTTGGCAGCACGTGCTGTTATCATG
TCTGTTCTAGGTACTTGACTCCATTCAAAGTTGTTCACTATGTAACTTTA
AAAAGACCCGAAAATATCCTGTGTTATTTTCTTTGTAAGGCTCCATGGTC
ATTTTAACTGTTTTTTTTTGTTTCATACATGTTCAGATACTGATGCACGC
GGTGTTATTTCTAAGATTATTAAGTCAAAAAGAAGGATGGTTTTACCTGC
AAAGGGTAACGTCAGTAACCCATTTAATGCTCAAAATGTGGGCAACCCTG
CGGGGATACAGACAATATCTAATGTTGTCTGCAGCGCCATTAAAGAGAAT
GAGCCTGTAGTTGTGAATGATAACATGGTTAAAACAGCTACACAGGAGCC
CTGTATCGAAAACTCGTCCAGTGCTTTGGCAGAACCTATTTCCCTTGTCG
AGGCTAGTGCTACACTGAATTTGGAACAACTTCTTGGTGGCTCCACATCT
TCGAAAAAAAGAAAACGCAAGAATAAGAAAGCTGATAAAAATGTTGAAAG
TGATGCTCAGTAAGTATTATTTCCTCTTCAAATACTCCTATGGTGTCAGA
AAGTTTCATTGCGCATATATAGAATGTCTTGTTCCATGTAATAATTGATA
CTTCTCCAGAAAAAAGTTGTGAAGTTTTAGTAGTGGTGGCATCAATGAAA
TTATCAGAGAAAATCTCAATGAAAGTAGTTCAATATATACTAAAGATTAA
GAAGTGGTTTTGGGGGAATTGATTTTAGTAGTATGACTCTTTTCATATTT
TAAATAAAACCAAAGGACTTAAGAGTAAATGACTTCTCTATCAACAATAT
ACAATACTCAGGTTGTCACCTACTGCACCAAAACCAGTGTTTTTCACTTG
TTAATTAAATTGAGGAACTTAGGCTTTTCATTAGATCTTCCATGTGTTAA
CAATCAGTGACTGAGTATTACTGCAGTACAGCCACTTTAGTAATTTCAGA
TTGTCATCTATTCCTATTCTAGTATCTATTTCTACACTGGCAGTAAGGTA
TGTTTTCTATAATGAGACACAGCGTCATTGTCTGTATTCCAGAAAAACAT
CTTAGTTGTATTGCTAATAAAACAGCTTCACAACTTGCAAATTGATCAGT
TATATACATGATTTTACTGCCTCTGTTGTCTTCCTCAACAGTTCAATTGA
TTAATTAAGCATGCAGATGATTTCTTGTTTTGATGTCATAGACTTGGGAT
AAACATGTGGGAAATGAGACGAGTAAAAAATCTGAGTTTAAAAGTTCATA
TCTGTTAGTGACTTGGTGTAATAGTGTAAGAGAATGTAAGTCCCTTGTTA
GAAAAGGTTTTGAGGTTTGGTCATTTTTAAAGATGCATTTTAGAATTTAG
AATATTTAACAGGTTACTATACTGTGACATGTAAATAGAACTCCTTATGA
ACTCCTATTTAGATATTATTGACAAGGAATATTGTGTTGTAGGCAATATG
CTTTATGATCTAAAAATTTGCAGAGAGTCTTGGTTTAGACATTTGAATTT
TAATGATATATATGTTAGATAATTTGTTTGCACATAACTATAGACTAGAT
AATCTTACTCTGTGTCATTTCATTTGCAATACCTACTTTTGCAAGTGGAA
CAGTTTATATGAATGTATCTGTAACGAATTTTATTTATCAAATTTTAGAA
CATTGTGTAATAATTGACACTATAAATTATACATCTACTAACTTTTAAAA
GTGCTATGAGGAACATACATTAAGAGGAAGATATATGATGTATAGCAGGG
ATATTTCAGTACATATTAGCTGTCTTTGATTTGTGGCAGGCGTAGCTTAT
ACAATCATGTTGAGTTACAGAAATCCAGAATGTCTGAGGAATTAATGATT
AGTTATTTTATATGCTCTGCATAGTAGTCTGCTGATTTGTTCTTTAGCTT
TAGTAGTAGGATGGTCTCATGTTTTAGCAAATTCGAGGATGGCGATTACT
TGAAAGCTTAGATTAGCATGTTCTGCTTTATGGCATTTACACATGCCATC
CGCAAGGTGAAGATCTCATTCTTTTAGTTACGTATTAGGTATCTATGTTA
AATTGATAGTTCTCTTTCTGATTTTTGTAGTCTTCTAGATAATTCTATTC
AGTCTGAGGTCAGAAGTTTCTTTCTAAGTGAACATCAGTACAAGTACTCT
TCTATTAAGTTAGTAATAGTTTTTTTTTTCCTTCTGGAATAATTAAATTG
ATCAAACCTCAGTGCAGAGGAGAGGTGATGGCAAGAGCACAATAACTAGG
TTTATGCTAAATACATGTCAATATTTTTAGCATTAATGTAATATTCATTA
GTTGTAAATTTGATAGCTGTAAAATCTGTGATATTTGATATGTAACAAGC
AGCTTTATAAGCCTAAGACTCCGGATACTAGAAATATACAACCAGATGGT
ATACATTCCTTGAAGATGTCTTGATCTTTTGGAAGTGTAAGAAGCAAGAT
CATGTCTCTAAATCTTTCACGGAGGCTGAATATAGAGCCATGTGAGCTTT
ACATGAACTTCTTTGGGAGTCGGGAGCTTCTCAAATTAATCCTACTCCAC
TCCATGCTGCTAACAAAAGTGTTATTGAAATTGTTGCAAATCTGGTATAT
CATGAATGCACAAAACACATTGAAATTGATTGCCATTATATTAGAGATGC
ATGTACACGCGGTGTTATTAAACTTCCTTATGTTAATACACAACTTTAAC
AACTGAGCTTTTTGCAAAAGCTTTGATGCGCCGACTAAACAAGTTTCTTA
ATGGCAAATTGATGCTTCTCCATTTACCCGCATAATTTTGAGTCTTTGAC
GGGGGATTTTTATATTTTTAGCGCTAGTGTACATTAATTGTAAATTTGAT
AGCTGTAACTTTATAAGCGTAATTAGAGGCTGAATAGGTGATATGATCGA
CTTATATTAAGGGATAAAGGTAGATTTCAGGCAGATATGGAGATTTTTTT
TTTTTAGAGTTCAGATATGAAGGGATTTGATAGCTGATTTGTAGCTCTAA
TTAGCTCTGCTGTACCTATAAATACATGAGCTGTTTGTGTGGTAAATCCA
TTCAGAAATAAAGCATTTTCTTATATTTGTCAATACAATTTTATTTAAAT
AAAGCGAGCTACTACATTAAACTGTAAGTTTAGGTAAGGTTCGAGCTTTG
ACGTGGTCCTTTATGGTCACAGGCTCACTGTTGAGTGCCCGTGCAACTGG
TTGATTGACTAGAATACATTTCTGCCTTGTTGATTATATAATTTTTTTGA
AGTTCTACTGTGGTGAAATATGTTCGCTATTTAGGTGAATCTTCCCTAGC
CAATGATATGATGAAGAGCAACCTGTATGTTAACTAATGTTAGTTGCTAA
GTTTAGTAGTGTTAGCTTCCCAATATGATTATTTATATTCAGAAAATTTT
ATTTATTTCCTCGTGCATAGTTGATACGTATTCATTCATGCTATTCCAGA
TATGGAGTTGGGTTGTATATATTACGTAACTTTTTGGGTGGTTTCTCAAG
TACTAAAATATTTCAATTAGCAGGGTACAGGTTGCTGCAACACCATCAAG
TCAAAATACAGCATCTGCAGACTATAGTGACCAAATTTGTCCGCCCAATA
GTTGTGCATCTCTACCAGGTGAATCAACTAGTGATTTTTTAGTATAGGAG
CACACTGCTGATGTTGCACCTTCTTTCCCTGACGTCTTTCCTACAATACT
ACGAATAGTTTGAGACAAGTGTATATTCTTGTTCTAGAAGCTTGGCTAAT
TCGCGTTCTTTGAACACTTGCAGGTTCAGACAATGCTGTACTGTTGGAAA
CCTGAATTATCAAGTGTTCAATGAACCCAGAAAGCTCTGGAACCTTTTTA
TCATTGTAATTGTGGATGTGGCTGAACTTGTGATGTTGTTGGCACTTGCT
GTAGTTTTTGTAGATGATGTTATGCAGAGCTATGATTACCCCTTCATATA
GCTTGTCGGTAGAGTTTAAGGATGGTACTATCAGTGTAGCTCTCAGAACC
ATGAGTTCTTGAGGCGGTAATTTAAAGTTGGGGATGGTGATTTCAAAGTT
CTTAGCTTGTCACATCATCACATACCTTAGTTCGACTGCAAATATAAATA
AACAACTTTGGTGATAGTAGAAATTTTGAGTTTCTGCTTGA
Sequence Length: 
8591
Sequence Checksum: 
a9dfca33f3df6b0699fbea413e4f13c7
View location in JBrowse: 
DCARv2_Chr7:31379970..31388560+
Gene: 
LOC108193292
Gene Biotype: 
protein_coding
Gbkey: 
Gene