LOC108192629

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108192629
Identifier: 
LOC108192629
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017372172.1, is a part of gene, LOC108192629.
The genetic_marker, MK003610 K1054, is located in gene, LOC108192629.
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_017372172.1XM_017372172.1mRNADCARv2_B18:332754..342314
Sequence: 
TGTATGATGATAAATTGATAGTTTGATACTGGTTTTTAGGGTTTCAGAAA
TTCAATTATTCTTGCTCTGTTGCAATTAAAACGTGTTTATACCAAAAAAT
AAAAGGGCAAGCTACAAATTGATTGATTCAACTCGTGTATGATTTTTATC
AACTCAGTAGACTAATGTGTACTTTCATCCAACATTAATGGGTGACCCTC
TTGCTCAAAAGGTTGGTCTCTATGTTTTTCTACTTGTTTGCTTCTCTTTA
TAATCTGGGCTTCTTGTACAACTTGATATAATTCAACTTATATTATGTGT
TATGAAAGTTAGTTTCTCTTTGGTGTGTGTGTGTGTGTGTAATTTTAGTG
TGAATTGATGTTATGAATTGTGTAGGTATTTGTATTTGGGTCTTTTTCTG
AAGAGGAGGCTAGAAACTTGCTGAATCCTTCGGCGGAAAATCCGGTGGAT
AAGAATGGTTTGCTGGCTGGTTCTTTAAATAATGTGCCTGGACTGTGCTT
TGGTAGTTTTGATGCTGACTTGAGTATAAGTCTCCCGAGTTATTCTAATG
GTTCGGCTAATTTTAAGCCCGAGGGGGATGAGGGGAAGGCTACTCAGAGT
GTGAATGTTAAGGTGAATGGAGATGTTGAAAATTCTTTACATTGCTCGAT
AATTGGTAATGGCAGTAAGGGAACTACTAAAGAAGATGAGTTAAGTGAGA
GTGTGTTAGATGATCAAGTTGGATCACTAGAAAAGCTGAGGCTGACGTCG
CAAGATCATAATGTGGTTAGTTTAAAGCACGGATCTCTTAATGGGACATC
TCATGGGAACTTACAAAAGCATTGTGAAAAAGCTTTTGATGGTCCTGCTA
AAACAGTCGAAGACCTGCAGCCTCGAGGGTTGATCAACTCGGGGAATTTA
TGCTTTCTCAATGCGACACTGCAGGCTCTTTTATCCTGTCCACCTTTGGT
GAAGCTTTTACTGGAACTAAAAAGTCATAGCATTTCCAAGGTTTGCTTCC
TTAATGAAAATGCTTGTGAAATCCTAATTTTTTAGAATTAGATTGCCTCC
TGTGCATATTGAAATTTTACATTAATAAAGTTCCAATTTTGTTGCTATAT
TAAAGTGGTTTCTGATAGTTATTTACAAACCCTAACATGTTAGAGTATAC
TTAGACTTCAGTATTTTGCTCACACACACACACACATATCAATATTTAGT
TTTTCATTCAGAGAACAGGACAGCTATTGCATGCACATTGAAATTCTGCA
CTTATATTTGGTCGGTAACTGAATGACACATGACTTTTCCTCCATTGAGG
GTATACATTATTTTTTATTTGGTAGAAAATCACGAAAGATGGATCTTAGA
GAATAAATGATGTATAATATCATAATACGTACATATCTAGTATAATGTGT
TTGAAACAATATTATAGAAAATTAACTGTCAGCTTTTCTGCAGCTAAATA
CAAGAAATTAAATTCACACTATTTTGGTAATGATTCCGTGATCAATCTTA
TGATGGCTGTTCTAATTTTACCTGTTCCTTAGGTTAATTATCCGACGTTA
GCTGCATTTGTGGATTTTGTGTCTGTTCTTGAACCCAATGGCATAACCTT
GAAGAAGAAAGACATACATGTGCTGGAGACTGGAAGGCCTTTTAGCCCTT
CGATGTTCGAAGTTGTTCTTAAAAAGTTTACTCCAGATGTGTCTAGTAGC
ATCTCAGGCAGGCCAAGGTTCATTCTCTCTTTTCTTTGTATCCCCCCTCC
TTTGACGGATCATTTGTTAATTTCTTTCATTGTTCATTGCACTCACATTG
ATAACTTAAATCTTAGCAACGTTACCTTGCTCCAGTTTATATCGGAGTTC
TGCTTTACATATCTGTATTGATGTTCTGATAGTGGTCTGTATTGATGTTC
TAATAGTGGTATCTTGTGTCTGGCATTTGGGTAAATAGATATGCAGTTTT
TCTATTTCCTTGCAGATGGTCATTTCTATATTCTGTATAGGTACATACAA
TGTTTTGAATATATAATATGTATCAATTCATCTTTTTCCAGGCAAGAAGA
TGCACAGGAGTTCTTAAGTTTCGTTATGGACCAAATGCATGACGAATTAT
TAAAGCTTGAAGGCAAATCAAGTGGGAATGGGGGTAAGTTATCTCTGGTT
TCTTCTTCAGATGATGATGAGTGGGAGACTGTGGGTCCCAAAAACAAATC
TGCAGTGACAAGAACCCAAAACTTTGTACCTTCGCATTTAAGTGAAATTT
TTGGAGGACAGCTGAGAAGTGTGGTTAAGGCAAGAGGTAATTTTATATTT
GAATTGAAACCTCACACGTGCTCACACACACACAAACATTTGGTCTTGAT
ATTTAATTTTGGACAGAATCAAATTGTATACTTTTCGTGTTTTTATATGA
TAATAATACAAGCCATACACTTTTTTTTTTTTTGACGGATAAGCCATACA
CTTAGATTCTTGAGAAAAGAAACAATATATGTGAATAGACCTCACCTAGT
TAACTTGGTGTTAATTCTGATATCCAGCAACCTGAAATAAATAAATTTTA
TCTAATGGCTGTAGTTGAATGCTTGATTCTGCAGTTAAATACGTTATTGG
TTTAGTTACATTTCTTATTTGGTAGAAGATAACACACATATTTTCAGTAT
ACTCTTGATATCTTAGATGGTGTTGTTTGCATAGTAGTAATGCTCTTGGG
ATAGTTAAGAAGGGAATGTAATGAAGTAGACTTGTAAATTTCTCACAGAA
CTTTGTCACAATCATGAACTAGAACTACTACTTATCATTGTTTCCTTGCT
CTTTATGCATGCCAGTTTCCTTCTAATATCTCTTGCTCTTTTTGTGTGAC
AACTTCATTTAAATAGAGACAAAAGAAATGCTCTTATAACAAGAAATACA
AGGCTCCCACTTATTTATTCATACTATTTCATCAATGCTATCAACCTTTA
CACTAATTTGTTTGGTAAAGCTACCATATCTCTGATACACTCCTTGTAGG
ACTAGAACCACTACTTCAGTGACGAAGACATATTGAGGCAAGCATCCATT
CTTCTTTCGATCCCTTTATTATTTGAACTTGAACCAAAAGAGTATCATCT
GATCCTCGCTTCATCTATTTTTCTGCCTCTGGAACAACTTTAGCCAACGC
AAAGTTCATTTCTCATCCATTAAAGAAAAATCACAATATTATACTTCTTG
GTCTTTGGTAGAGACACAAATATAATAACAACTTTGTGCTCAACCTTTAA
TTTTAACTAAATTATTCAGTTGGTTAATCAAGCCATCGAAATGGTTCAGA
TGAACATACTTGATTGTTTATCTTGATTTTAGGTGCAGGGGTTAATTAGA
TAGTTGAAAATTACTTAAAAGTTTACTTTTAGGTAAAAGGTGACTTATAA
GTCGAAGTCTGAAAAGAACATATGCTGTTATTTTTAGTTACTCTGAATCT
TACAATTTGACTCAAAAATAATTTATACTAATCGCTAGATCTTATTTATA
TTTTGTTAGATAATAAGAAATTTATCCAAATAAATGGCAACTTACAAGTC
AAAATTATATCTTACGTAAGTGAATGATAACTTTCTCTTAAGATAGGACA
CACGGGCCTTAAGTTAGGGGTGTCAGACTTCCACAGTACTCCGTGTACTT
GCTCCCATTTGATTTTTTATTACTGTAATAGTAGATACATCAACTACAGG
TAGTAGAAGAATTGGAGGAAGTTTATAATCTTATTTATAAGTAAGAAATA
GGGATGGGGGGAGAGGAGATTCTTAAATTTTTAAAGAGCCACTAGAAGTT
TCTTGGAGCATTATGATTGCACACACTCCCTATATAATTTAAATTGGGAG
CCTGTATAAGGAGGCTGTCACAGATGCTAACGGGGGTGTATTCGATTGGG
ATTTTAATGGATTGTTTTTAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
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nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnAAAAAATGCTTTAAAATCCCAATCCAATA
CACCCCTGTAAGTATATATTTGACTCGGACATATGAGATGCCCAGGTCAC
AATTAGTATATGTTATCGTGTGGTTGTGGTATAATGAATATGCGGGGTTC
CCAGTTTGAACTATATTAGCTTTTCCTAGCAAAGCTGTATATCCCGTGGT
TGGGTATGCCCTTAATTCTCAATCTTGAGTTACTGCATCTTTAAAAAAAA
GAGTAGTTGATGCATATATTACATGCACGCTATAGCTTGCTTTGGTCTAC
TTTCTAATAATATCAAAAGGGATGCTAGACGGCTCAAGTTAAGAGATATA
GAAGGAAGAAAACAGCGGAGCTTGATAAAATTACAGAGACTATGCTTGTA
TATAGAAATTGTAGTCTGAGGATTATAAACGAATGATTCTATTCTCATCA
CTACTGATCTGTGGATTGTAATCTTTTAAATAGTCAAGTCACATGTTTGT
TTTTCTCAGAACGAGGGATGCAGTACTTTAATCTAATAAAATATCTGTTC
GGAGAAATTATTTAAGTTTTTCTTAGAAGTCGGTATTTAATCCGTTCTAG
TCCCTGGGCTATGATCCCAAATCCCAATTCCCAAGTTTCAAAGACACAGA
CTAGGATTATATGCTTTAAACAAATATAGTCCACTTCCCGACTAAATATC
TTGGAACAACCAAAACCAAAAAGAAACTAAAGTCCTGATCATGAAGGCAT
AAAGTGATAGATATTGGAATTTGGAACTGATAAGGGCAAGAAGGAACTAA
TAATTAATCGGAGTGAGGGGGAAAGTGGCTAATTATAGAGTAACTGAGTT
CTCTTTATAAAATCTAAAGTAAACGTATCTAATTCAGCTTGATTTAGCTC
AAGATAAAGGAGAACCACAACTTGAAATGCTTATGAACAAAAGAAAGGAA
TTACTTTTCTGTCCAACTTTTATATTAAATACTAAGTACTGCCTTCATTC
TAAAATCTGCAAGTCAATTAAGCTTTCTTACATCTGTAGTGCCTTTGACC
AATCTTTGATGTGGGATACTTGATGATCTACAAAGATATTGATATGCACT
GGATTTAGTGGAATTGAATTGACAAAATTGAGGGGTGCCAAACTAAGACT
CCTCCAAGTGTATTCGACCACTCATCTTTTCCAAGTTAATTTGACGTAAT
GTTGATGCTAAACAAACATAAATGGTTGGTGTTTGTAATTGTAAACCACA
AGATTCTTGCATCTCCTTTTTACCACTCTTATGCTATTACTATATGTTGT
GGATTTGCCTGGTTTTCTGTAACACTTTTCACTGTCAGCATAGCAATTTA
AGGTTGTTTATTGCTTAATCAATTTTTTTGTGTGTATAACAGGCAACAAA
GACTCTGCCACTGTTCAACCATTTATGTTGCTTCATCTTGATATTTCTCA
TAATGCTGTTCGTACTATTGAAGATGCTCTTCATTTATATTCTGCACCAG
AAACAATAGATGAGTATCGGGCATCAACCACCCAAAAAGTAAGTTTTTTT
TCCTGTTTGCTATTCTAAGCACTTTGTGAGTGGTGTACGGTATTCAGATA
TTCGTGTATTACAATGGTATACGTTTCAGGTTGGAGTTGTTAGTGCCAAA
AAATCTATTAGCATTCAAAAACTACCAAAAATTCTGATCCTACACCTGAT
GCGCTTTGGCTATGGAAGCTATGGAAGCACTAAATTGCATAAACCTGTGC
GGTTTTCTCTTGAACTCTTACTGAGCCGTGAGTTATTGATGACCTCTGCC
ACTGAGGTACATAATCTGTCTTGCATTATTCCTTCACAATATTTTGAGCT
TTTCTGTATAAATGATATCTCAGCAATGTTAGTTAGTGAAAGAAACCATT
GTCTTGTCAGTATATGCTGATATCCATAATATCTCTTTAAATCTGGTGTT
AAAATTTGAAATAAGGAGATACCTAATGCAGAGAAATTTTGGGTATTTAA
AAATTATTTCTTACTATAGCACAATAATAATATTAGTAAATCCATAAAGA
TATGTACTCAAGTGTTGCAGTATACTATCATGGCTCGCAGAGAGTAAATT
ATTATCGAAATCCCTTATGTTATTTCTAAATCTATGGTTCTCCCTCTTAT
TGTCAATATTTGATCTTTTATATATGTACCACTCACATTCTTTTTGTTTT
TTCCAGTTGAGTTCTATAGTATAATTGCTTTTTGGGTTTATTTACTTGTC
TGGTTAGTTCATGTTTTAGTAGGTTCTGGTCTCTTTGTTGTTTATTTTCA
GGTGATTTAGACTTTTCTTTGATAAAATTGGTGGTATCAAATGGTAGTTA
ACGCTAATTGTTTATGTGCGCGAACTTATCCCGGTATCAAATGTTATTTA
ACGCTAATTGTTTATGTGTGCGAACCTGACCCTATCCTGATGACCCTTAC
ACATGGGGACATACTTTTCACATGACTATGATATAATAGTATGAGATATA
AAGAAAACAAGTTTAGAGTATATTTTTGTCTAATACCACCTCTTTAGCAA
AGGTCTCTCCTTTGAAAAATCCACATCATTATCTCTTCTTGATCTCCGTC
TTCTGTTAGTTCTTTTCCCTGAGAAGCAATTATCCAATGTGATAAAACAA
ACTAGGTTGGGGCTTCTGGCAATATTCAATATTCATATAACTAGCTTATA
ACCCGTGCAATGCACGGGCGGTTAACATATTTATTATTTTATCGTATATT
TTTTAATTTTACCTAATTTATTGTAAAGTTAAAATTATGATAGAATAATG
TGGTTACATAAATATTTTATTTAACAGTTGGATAAACTCTTCATAATTAA
GTCCGTCAAATGGCATATTAAAAATTAGGCCAAACATATATATTAATGAA
AATGTTAAAATATTTTTTTACATGTTATAGTTTAAGTTGGTTATATAGAT
AGGCCCGTATTTTAGCTCAAGTATCGACTAATCAAATTTTTAATGTTTCG
GTTAAAAGATAATTTATTTTAGTTTAAAAGAATAATTGGTTATATAGATT
GGTCCGTACTTCGGCCAAGTACCGACCACCCGACCAATATAATAATACTC
CCTCTATTTTTTATTATTTGACGTTTAGTCTTTTGGCACGCATCTTTGGG
TATAAATATGTCGTCCATGTCTGTATTAATTGTAAAAGGTTGATTTTTTA
GTTAGAAAATTTATAAAAAGATAATATATTTTAATCAAAATAATAATTAT
CATGTTTCTCAATGTTATTTTAGAAGATTGAGTTTTTTAGTCAGAAGTAT
AAAAAAGGTAATATATTTCAATTGAAAAGAATGATTGGTTATGGATAGGC
TCTGAATAATTGGTTATATAGATAGGCCCGTACTTTGACCCAAATTAAAA
AAAATAATTGGTTATATAGATAGGCCCAGAATAATTGGTTATATAGATAG
ACCCGTACTTTGACCTAAATTAAAAAGAATAATTGGTTATATAGATAGGC
CCGTAATTTGGCCCAAGTACCGACCGACCAAACTTTTAATCTTTCGGCTT
TAATAGTATAGTATAGATTAGTACATGAAAAAATTCTCATCCCAATCTGA
TTGTACATAAGCAGTTAATCACTTTCTATCCCACAGATGTCCTCAGATCA
TCACTAATGAGTTTTAACCTGTTTTTCCACCAAACATGGGTGGCCCATGT
TTTACTTGCAGTAGACACGTTGGTAAAACCAGTGATTTGTTCTAGCAGAA
ACTAATCACACTCATTTTAGACGTGTAGATTAAACCAGTGGTTTGTTATA
GCAGAAACTACTTTTGAGTGAAGTCTGGTATGTTTTATCTGTAGTAATAC
TATACGCGAGCGTTTGTGGTAGCTATTGCTATAAAACTTCATTTTCCCTC
TGCTTTCAGCTGCTAGGAAAGTCGGGGATGAAAATATGAGGGTTCAAGTT
AGTCTCTCCTAGTTCCTCTTTAAATTTCAAAAATGAAACAAAAATGAAGT
ACATTGTTGTATTCATTTTTTCATACTTTAGATTTGCATGGAAATGACTA
TATTCTCCCCATGCATAAGTCTTGAAGACCCTTGTATATAATATTTTAAT
TTGGTCATAGAAGTGTGACTTGTATGCATATGGTCATTAATGTTAGTAGG
AAGTTGGTTGTACTTCATAGTATTACCCTACCCACTTGTATCTTTAATGA
AATCAATCAACTGTTTCCTGATTCTATATGTTTTTTAATGTGGCTTTACA
GAGACGAAAATATGAACTTGTTTCGACTATAACACATCATGGGAACGAAG
CTTCCAAGGGGCACTATACTGCTGATGCTCGTTACCCCAGTGGCCAATGG
TTAAGATTTGACGATGCCTCTGTTACTGCCATAGGTGCAAGCAAGGTGTT
GCATGACCAGGCCTACGTCCTCATCTACCAACAATGTTGACAGGGTATCA
AAAATCTCATTCTTAATCATCATATGTAGGCCAAAGAGCATAGGTATTAG
TGAACTTAGATATCCAAATGTGCGGCCGTAAAGGTTGGAAATTATAAGTT
ATCAATAGATGTCCAAATGAGTGGGTGTAGAGGGTTGGAAAGTACAAGTT
ATAGGTTTCCAGAACCAGTAGTTATGTGTCATATATACAGGGTTTTCGTG
TGTGTGTGTG
Sequence Length: 
9560
Sequence Checksum: 
6cce2dd60cfa6c09414ad676f18c886b
View location in JBrowse: 
DCARv2_B18:332755..342314+
Gene: 
LOC108192629
Gene Biotype: 
protein_coding
Gbkey: 
Gene