LOC108205433

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108205433
Identifier: 
LOC108205433
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017375389.1, is a part of gene, LOC108205433.
The genetic_marker, MK001028 GSSR-029, is located in gene, LOC108205433.
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_017375389.1XM_017375389.1mRNADCARv2_Chr1:14957068..14965759
Sequence: 
TTATTTCACCAATCACATCCTCACCACACTCCACTCACTGTGTTCTCTGG
GCTCTGTATAAATACATACACACAGTTACTTACAATCACAAAGTCTTGTT
TAAGTCAAGTAAACATAAAGATGGTGGAGAAGACAAAGATGGTGGTGAAG
GAGGAGAAGACCCAAATGGTTCACTCACCCATTCTCACTTACTTTTCCAT
GCTTTCCCTTCTTTCTTTGTGCCCCCCTTTTGTTATTTTACTGTAAGTCC
CTTTTCTCTGTATCTATATGTGTTCTATATGGCTTAAAGTTTTGAACTTT
TTGTGGGTTTGGCTTGTTTCAGATTGTTTATTGGTTTAGATTAATGTAAG
GCTTGAATCTTATTACAAATTTGTATATGTATGTACTTTTGTGTGTGTAC
ATGTCTTAAAGTTTTGATCTTTTTGTGGTTTAGCAGGTTTTAGATTGTTT
ATTGGTTTTAGATCAATGTTGGGATTGAACCTTATCACAAATTGAATTTT
TTTTGTTAAATTGTGTGTGTGTGTGTGTGTTTATGTGTTTGATTTGGTCA
ATAAGTACAATAAATATGGAAGTAAGCTGGGTTGAAAATTAAAACACAAC
TAAATTGGTTGTGAATTTTGCGAAAGAATGGATCTTGATTTGCATCAGTC
ATTGCATATTAAATTCTTGAAATTTTGTTTTTTAAGGAAGAATGAATCTG
AATTTAGTGGTTTCCTGAAAGACAATGAAATTTGAAGTGAATAATGAATT
TTTTATTATCTAAAATGAAAATCATACTTATACAGTGCATATGATTGTAT
GCGATGCTTTATTATTTATTGAAGCCTTACTATATAATGAAATAAGAGAA
AAATGAAGAAGGAATCTTATTTGTAAGAGAGCAATTTTATAAGCCTTTGG
GATCATTGCTGCTTTTAGTTATTTCAAGTAGACTGTTTAAATAAAGATAG
CTGGGCATCATGTAGAATAATTTCAGAAGATCTTCTGTTATCCTTGTGCA
TATTACAATACTCAAGGTGACAGATGGAACACTTGAAACTTAAAACTGTG
AATATGCTCCAGGAAATTTTACACCTATATGAAACTGATTTTAATCTTTC
ATGGTTTTAGAGGTTCAGCTAATGATCAAAAAAGTACCAAAAGCCTAATA
TTGTGCAGGGATGTATCTTTGAACAGTTCAAGCATCCCGGTCATATTAAG
TTCATTATTTTTTATCTGTTACAGTGCGGTTTAAATAAGGTAATCTAATT
TGAGTTCGATACTACATGTGCAGATGGTATACCATGGTTCATGCTGATGG
GTCTATATATCAGACATTTGATTTGTTCAGGCAGAATGGGCTTCAGGCAT
TTTATGATATTTGGCCAAAACCCAGTATGACTGCGTGGAAAATTATATTT
TGTTATGGAGCTTTTGAGGCTGCACTTCAATTGTGGCTACCTGGAAAGAG
AGTCGAAGGACCAATTTCTCCTGCTGGGAATAGACCTGTCTATAAGGTAG
ATGAACAACAGATTCAGTAATGTAATTGATTTCATTTCCAATGCATTAGT
TACTAGTAGCTACACATCAACATTTGCAATTTTGTATATTCAATTTATTT
AAAATTTATTTTTGCATTTGCTACTGAAATGAATATACAGTAATACCATT
TTGCTAAAGATATCTAATTTCATAAAATTGAGGTCTTTTGATGTCTACAA
CTTTTTTGGTTCTTTACTTAATTGTAGGCGAATGGCATGGCAGCATATGC
AGTGACATTAATTACTTACCTTAGTCTTTGGTGGTAAGGATTCTTCCCTT
AACCATGTATTCAGATGATTAAGAAAGCTAGGATTCGTACATAGATGGTC
TAAAGTTGCAAACCTTTATTCTATAAGTATGTAGTGACCTGGTATATGGT
CTGCTGTTTTAGTTTTTCTGGGGATGATATAATAACTGTTTACTGGTAAA
AGAATACCCAGTATTGAAAAAACTTGTTTATTGTTCTGTATCTTCTTGGA
CTTGCAGGAGAAAGTTGTCATTGTTTATTGTCTATATGTATGGAAATTGG
AAAGTATTCTTTACTCAAGTTTGCCCAAGCTAAAATAGATTATTGTTTTA
TTGTCAAATTCTTTGCTTCTTTGCCTAAACCATAAGCTTATTATATCATT
TCTAGCAATCGCCGACTTGTTCTCTATCCAACGCATAAATGGCTGAGATT
TCACATTCTCAACCTCTTTGTTAAATCGGGCTCGAATTAACAATGACGTT
GATTTGCACAGATTACTTTTTCTTTTTGGGTGGGGTTGGGGAAGAGGGGG
GACTGAGCTTCCCCGTGTCTGTATAAGAAGGGACAAGTTGATAGAGCATG
TAACAGTATGTAGTTTAGACAGTTACAACTAGGATTAAACATGTTCCTCT
GGCTTTGTGATTTTAGGTGTTAATGCTCTAGTATTTCGGGAATATTTCCT
GGATATCATAGAAATAAGGAACCTGCAGTAATACTACTTCATGCTGCTTC
ACTTTAAGTAGGATCACATAAATTATTTATGCATTAGTAAATGTCGGAGA
AATCATGCTTAGTTTTGTCTGATGACGATTGGGAAGTGGTCGGAAGTCAT
TTTCCTCTTTTCATTATTTATCTTCAGGCTTTGATAGTTTAATTCTAACT
GCCTTTACTGAATACTGGTTATTTGCTAAATGAGTGTTTTCTTAACATTC
ATTATAATTATCAATTCAATGAACAACCTTAGGAGATACTGAGATAGGAA
CAAATCCCGATCGTCTGTATCTACATAAACATGTCAACTTCTGATTTCTG
ATTTCAGTATAGTAATATCAAGTGTCACACATAGTATTTTTTTGAAGTAT
GCTCTAATTTGTGTACAGGTTTGGGATATTAAACCCTTCCATTATCTATG
ATCATCTTGGAGAAATATATTCAGCCCTTATTTATGGCAGCTTCATCTTT
TGTATTTTGCTATACCTAAAGGTGAGATTAGATGCAGCAGATATTTGACG
TCCAGTCGTCTAGTATACATTTGCCATAGTAAATTATTCGTATTTCTAAT
ACTTGTGTTTCATCCCATACTAGGGTCATGTGGCACCATCGTCTACCGAT
TCTGGTTCATCAGGCAATGCAATAATTGATTTCTATTGGGTGCGCATCCT
TACTGGTCTATGTTCTCTTGTCGTCTGTCTGTTTCCTCTTTCTTTATTCT
AGAAAGACATTTATTGCTTCAATCAGTTTGTAAGTGCTATGTTAAATGAA
TTGATAGGTAAGCAAGAAATTCTGCGTATGAGGATGAACAACTATTGTTT
ATGATATTTTGAAGAAGATAAAACCTGTTATGTCTTGGGAGCAATATATA
TGAGCTCCGAGCCTCTATGCATGTTTTTATTAATTATGCTGCCACATGCA
ATCCTAAAATTGCTTGCCATGCTTCCAGTGAGCCCATATATGTGATAAAA
TCTTTCAACTTCTCTTACATTCTCCATTCTGAAATTTTAATGAATTCTAC
ATTGTATATTTAAATTCTCTACATGGGTTGTACTAATTTGGAAGTGTTAG
ACCACTGGAATTTGTTAATTGTTCAATAAATCGAGAGGTATCCAAGCGAG
AAGCCCTGTGTAAGAGGTTGAACAAATATTTCTTGTTAGATTTGAAGAAA
ATATAACCTTTTATGTTTTGGTAGCTATATATTTGACCTCTGACCCTTTA
TGCATGTCATGTCTTTCATACCAGTGATGCAACTGTAAAATTGCTCGTCA
TGCTAACAGTGAGCCCTTGTACACAAGAAAATCTTACATCTCTTACTTTC
TCCATTATGAATTTTTGATGCACTCTCCATTGTAAATCAAATTAATCTTC
ACGGGTTGTGGTCCTAATCAAAAAGTGTTGGATCTCATATGATTGAATTT
TTCTGTCCTTGCCATCCCCTTTTATTATGTTCATTAAAGTGCTTTCTAGC
ATATATGATTTTCATGATGCCTGTAAAAGCATAAACATCAACTTGCGTTG
CTTCTATCTACAAATTAAATGATATCTGAATCCTGAAATTACGGAGATGT
ATATTTTTCTAGCAAGCATCGCATGCATTAGAATGTGTTGCAGACTACTT
GATTATTCTTAAAACACCTACTATTCATCTGAAGATGCATAATGTGATTC
ATTTCTCCTGCTTATTATAGGGTATGGAGCTATATCCTCGCATCGGCAAA
AACTTTGATATCAAAGTGTTTACCAACTGCAGATTTGGGATGATGTCTTG
GGCGGTTCTTGCTTTGACTTATTGCATAAAGCAGGTATGTGCTCGAAGGC
AATTTCTACTAGTTATATATGTTGCAAAGTGTATATGATACAATAACTTA
TCAAAATTCTTGTTAAATCTATGTGCATATAATTGGTTGTGCACCACCCA
AGCATCTTGCTATCTTGTACACCTGTTATACCAATAGTTACATTCCCAAA
AAAATTGTAACAATCTGGAAGTATAACATACTCAAATAGGCTTCGAACTA
TTTTTTTCTGTCTTTACTCTCAGCAAGGGTATAATTGTCAATAATTGACC
TCTAAATATTCTAGTAGCTACTAGCTAGTAGATCTTTTTCTGCTGGTAAC
TAAATTGAGTAGGATATCTCCTCCCAGAGAAGCCAGTAGATTATGAATGG
AGAATGGTTTACTTGTTTTCTATTTGATATATAAGCAATGAATGCATGCA
TTAAACATTTGCTGCATTTTTCTCTCTATAAAATGTCTGATTCTATCCTT
CCTCCCGATCTCTATTCTGAAAATTTTCCATCTTCTGTTGCTTCTTTAGA
ATCTCGTCAGGCAAAGGTAAGCCTGAAAACTAAGTTTTGTGTTCACTATG
TAACAGTATGAAACAAATGGAAAAGCATCTGATTCAATGCTGGTAAACAC
TGCGCTAATGCTAATCTATATTACAAAATTTTTCTGGTGGGAAGCTGGAT
ACTGGAATACCATGGATATTGCACATGATCGAGGTATATATATGTATGCT
TTAATCTTTCAGTTTAGTGTCTAGATCCAGTATTTGCTACTATGTCTGTT
TCTAGAAGTAATACTAGTCTAGGGCTAGTTCTACTACTTTTGAACACTCG
ATTATTTTAATTTCTTTATTTTACCATGAATTATATGTTAAAAATTCACA
CCATATGGAGGACTGGTAATTTTTCTAGAAAATTCGGGGACAAAATAATT
TCTCTTGAATGGTTAAAGGATAAGAAATAGTCCAAAACAATATCTAAATG
ATTATGCGAGATTACAAGAGTTCTGGTCTTGCATAACCTCTCTTATCCCA
GCCCTTGCTTTTGGAGGCAAAATTGGCTTTGTCTGTTGTTACTTACATTT
TCCCTTTTTATTTCTGGACAGCCGGTTTTTATATATGTTGGGGATGCTTG
GTGTGGGTTCCATCTATCTACACTTCTCCGGGCATGTACCTTGTTAATCA
TCCCGTGAATCTTGGAATCCAAGTATGTAACTGGTCTGGCACTGTTGATA
TGGTTCCAAAATGTTTAAAACCTAAGTTTTTTTTTTTTTTACTTCTGTTC
TTGCGCACCAAAAGTGTTGAAATTGCCCTTTTCCGGTTGTCCTTGAGTCA
CTGTTGGATGATTATAACTTGAATAAAGGTGACAACTGACAAAATGGCGG
TAGATAAAAATATTTCAACTAGATAGCTGGCTAGTGGCAATGTTTAATTA
CTTGCCAGAGGGAATACTTTTGCGATTATTTAAATGTCAGAGCCCTCTAT
AAATGAACTGAATTCCACCCCCTTCCCTCACAAACAACCTAAACGTGATA
AATTAATAATAAGAAAATAAGTTACCGGGGTAAACCTGTGAAAGTAATTT
TTTCTTCTTCAAATTGCATGTATACACACAATTTAATGACATGAATTTTG
AATTCACGAACTGACCAAAATTTTGACTTCCACGATGAGACGAGTCATAT
ATTTTGGAATGTTTGAAACACAAAGAAATATTTTGACTGGAAAACTGTTT
TGCATAGCACAATAAAATTTTAGTTGTCCCAGTAATTTATTTATGGCTCG
TCATCTTATATTTTGGACCGTCATAGTCCCTTTTTAAATGTGTCAAATGT
TTAGGCTGAGTTTGATACATGTAAATTGATTAGAATGAGAAAACCAATTT
TAAGAACTTACTTGATCTGATATGGACTGTGATTATAATAACCTAAGTGA
CCTGGGTGCCAAAGAGAGGCTAACAGATCTTCATTCTTTCTACAGCTTTC
TCTGTATATTCTTCTAGCAGGCATATTATGCATATATGTCAATTATGATT
GCGACAGGCAAAGGCAAGAGTTTCGTAGAACAAATGGGAAGTGTGTGGTT
TGGGGAAAAGCACCATCAAAGGTAACATATATGGAGGGCAACTTGACTCG
CACAAGATCACTTGCTGTGAAATATTGATTTTGTTTTCTTCCATGTGAAT
TTTGTTACTCACTCTTGAAAAGGGATAATTTGTTCGGTATCTTACACAGA
TTACCGCTACATACACTACCAGTTCTGGTGAGACAAAAACCAGTCTTCTC
CTGACTTCAGGATGGTGAGTATATATATATGCACCGCATTGTATCTGTCA
CACATAAATAAGGTCACATATGATTGAAGATACTAAAAGTAATTTTTTTT
ATCGAAGAATAGTTTTTTATGTAATCTGGAAAGGAGTTCTGTGTGAAGTA
GGCACTATAATATATGTGCGAGTAACTAGCTTGCTACAATCTGTCTGTAA
TTTTTCTACGAGGAATTGGTAACTCTTCTTAAATTATATGGATCTTAAAC
AAGTAAACTAAGTAGTGAGAGGATAATTGTATATGAATAGTGTAAAAACA
AACAATATCCTACAAGTTGTTGGTGAGGGATCTTTAATTCTCTAATCCCT
AACTAGTAGATGCTAATGTAATTATTAGGTTAATACAATAATCTGTACTA
AGACAAGACATAGGTATCTAAATATTATGTACAATCAAGATTGCTTTGCT
AAAGGACCTGTTGAAGAATCTACCTAGATAAAGTACGGATAATAGTAGAG
TATGTAGTTGGACTTTTAATGGACCTCTGATAGATGCAAACTATGTTCAT
AATCTCATCAACATGCTGTTATTAAGAATCTCATTTCAATATGAACAAGT
TCAAATATATATTTGTTATTTCTGTTTTTTTTTCTAAGAGATTATTGATG
TTTACCATTATTAGCTAAAATAGAGTTGTCATTAATAAGCGTCGTGCTTT
TCTTGGTATTTAAAAGCAGGTGNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNGTTGTCATTAATAAGCGTCGTGTTTTTCTTGGTATTTAAAAGCAGGTC
TTATATTTGCCTAGTTTGAAGTTAAAGTATTTAGCATGATAACTATTGAT
TTAACCTGAACCTGACCAATTTATGTATCCATGAGGTGATTATAAATTTC
TAATAAAGTATGAGTTTATTCATGCCCAGCACACTTTCTGTGTTTTTCCC
TTCAGGTGGGGCATATCTCGTCATTTTCATTACTTGCCAGAAATATTGGC
TGCCTTTTTTTGGACAGTACCAGCTCTTTTCAGCCATGTAAGAATTAATT
GCAATTTGAGAGAGAAGTTCTCCGTATTTTTTATACAGGAGCATGCTAAT
ACTATTTTTTTTCTTGCGATAATTCTTTTCTGCAGTTTCTACCGTACTTT
TATGTTGTCTTCCTTACCATCCTTCTTTTTGACCGAGCCAAAAGAGATGA
TGATAGATGTCGGTCAAAGTAAGCAAATTTCTCATAACTCTAGTTTTTAT
CTAAAACTGTTGATACCTATCAGTTAATTAGCATAAGAACAGATAAATTG
GAACAATCTTCTTCATCTTCTAGTAAAACAGCAATATTATCTCCCTATGA
TTCTACGCACATGATGATATAAGTTACCAAGTTGCAAATCGATCTTAAAC
AATTGGCAATGTTATTCACGGATCATATAACATCTAAAATTCATTTGATC
AAACATCGGTAGACCGGAAGAAATGTGGTAAAGCTGGCCACTTACTGTTT
CTTCCTGGTGCATTATTTTGCAAACATCATTGTCCAAGAATTGTGATTAT
ATCGAACTGAGCTTTGTATTGGTAATATTAATGAACATCTCTCAAATCAT
ATTGCAGGTACGGAAAATACTGGAAGTTATATTGCCAAAAGGTTCCGTAC
AGGATCATACCAGGCATGTACTGAGTGTTTGTTGTATCCATTGGCCAATA
GTCGACCATCGACTATGATCCATCTGTGGGATCATTACTATTAGTATGCT
TCATCTTTATAAGCCTGTACCTATGGAACAGGTCTTGTAAGCTTAAAATT
TTCAACATAATAATGGTATCAGGTGTTTTTAGACATTTTGTTCTGCATGA
TCTCATCACATTCAGAGTGTCATTGCCAAAGTTTTCACATA
Sequence Length: 
8691
Sequence Checksum: 
83de58522835b2c7b049b0b20dba89a8
View location in JBrowse: 
DCARv2_Chr1:14957069..14965759-
Gene: 
LOC108205433
Gene Biotype: 
protein_coding
Gbkey: 
Gene