| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017368053.1, is a part of gene, LOC108200002. |
| The genetic_marker, MK003701 K1145, is located in gene, LOC108200002. |
| Name | Description |
|---|---|
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 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 | |
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. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| XM_017368053.1 | XM_017368053.1 | mRNA | DCARv2_Chr8:22527223..22533876 |
AAAAGTTTGATTATTCGATTTCCTCCCAAGTCCCAACTCCTCAGCAGAAA
ACAGTAGTAGCATTAAAGTTTAAAGGTCTCGGCTACTAAAACCCTGAGAG
AGCGAAAGAGAGCCACAGTAGAAGAAATGCTCTCGCGCTTCATATCAAAG
CCCTTGCATCAGAATCTCCGTTTGATCTCATTCTTAATCTCATCTCATCC
CCACCCTCCTCCCACTCCTACTCATTTCACTTCTCACTCTCCCCAAACCC
ATTTGTCCCCAAACCCTAGTTCGTCTTCTTTCACGCATTTCGTCAAACAC
TTCTCCACCAACAACAAAAACAACAATGGGGATAAGACTTCTTGGAATTT
TTCTTCCGAAATCGAAGATTCTTCAAGTTTTGGTGGGGTTTTAGATACTG
ACGAGGCTGGGGGTGATTTCTCTAAGCCCGGTGGCGCGGTTGGGAGAGAT
TGGGTTATTGAGAAGGATGAGGATGATGAGGGGTTTGACTTGTTCAAAGA
GGTTGAGGGGAGTGTTAGGGAGGTTCCTAAGCTGGGTACCGTGAATCAAG
TTTGGCTGGATGACAAGGGTGATGATGAGGGTCTTGATTTGTTTAAACAG
GCTGAGGAGAGTGTTAAGGAGGTTGGGGGTCATGGGGAGGAGGAGCAGGA
GAATTGGGCTACGGCCGATGGGTACCAGCCGTGGGATTTGGACAGTGAAG
ACAAAGGGGATGACGTGTTTGGTTTAGGGGAGACGGAGATGAGTGGGGGT
GTGGAGGGAGAGGTTGGTGGTCAGGAAACTCAGAAGAGTATAGAAGACAG
GTTGTTACTCGAGAAAGAAGAGAAAGAGCTTTCCGTTGTGCTTAAAGGTG
AGGTTTTTAACTCATGGATTGGTTGTTTTGTTTCAGCAATTTATGTTTGT
GTTTATGATTTTTAGTTTGTACAAGTATGTAAAGTTTTGATGATTGTTTA
TGTTATTCTTGAATTACGTTAAGGATTTGTTTTTTACATGCGGTCTTATG
AAATGTGAGTGCAGGTTCCTCTGTTTGATGTGTAGTTGTCAAATTATTCG
GTAGACATTGGTAAAGGAAAGAGGGCATGGGGTCACGTCTCATGAGTCAT
GACCACCTAAGTGGAGGTTTAGACTGGGTTAATCATTTATTTGATTGTTG
AGTCTATAGCCGTACGAGCAACTGAACATTTTCAGAAGGATTAATATCTG
TGTATGTTAATGTAAATAAATTTAATGCAACTATATATATGGGATTTGAA
GTAAAGTTTAATAATTTAGTCTTCAGAACAGAACAAAAGTAAAGCAATAG
ATGCCATAGCTTTATGAAAATAGAGCTAGAAATGATATAAAAATAGTGAT
AACATATCACTGATATTGAATGCTCGCTGTTGTTTATGCGCATTGTTTGT
TTAATAAATATATTGGGTGGAATCATTTATATAGAACAGTCGGAAGGCTG
CTAGATAACACATAAAAAAACCCGTGATGTTTAAATTAAGTAAAGATTAT
TGTTGTTGCAGGTCCAGATCGTGCTTTTGGTGACCTGGTTGCCACATCTG
GAATCACAGAAGAAATGTTGGAGAGTTTGATTGCACTAAAGGATCTGGAA
GGAATTCAAGGACTACCTCCTCTAAGCGAGATCGAAGATATTCGTTATGA
AAAGAATACTAGGAAATCTTCTAGGGCTGATATAGAGCGTCTGAAGCAGG
AAGAAGTTGCCAATGCACGAGTGAGGCAAGTGGATAGTAAGGGAAGGGCT
TATGGAACAGGAAAGCGGAAGTGTAGCATAGCTCGTGTTTGGATTGAACC
TGGAGAGGGTAAATTTGTAGTCAATGACAAACAATTTGATGTCTACTTTC
CTATGCTTGATCAGCGGGCTGCTCTTCTTCGTCCTTTCACTGAGACAAAG
ACTTTGGGTCTTTGGGATGTCAACTGTACCGTGAAGGGAGGTGGTATCTC
AGGTTAGTTATCTTTATGCAAAAATTCATCTTAGGTCACTCTAGATGAGT
TAGGTTCTAGTATCTCCTTTTCTCTTTGCCGTAATTTGAAATTTTGTTTT
CTAGTTAAAAACTGCAAGTCTGTTTCAGTTCTTTCTCTCTGTCTCTTTAT
TGGTCTTGTGGGTGCATCTGCTTTTTGTATGCTATTTGTTATTTCTTTTT
TGTGCTAGCATTACTTGTAGTGCTTGGTGGGAGCCCTCTGCTAATTATAT
TGTATTTCTTATATATAGAAATATATTGGGAATATCAAGGGTTCTCTAGT
AGTCTTTTCTCTGGCCTACAAAAGTAGATCCCATCTGTCCTGAATTGGTT
TCCTTTCGTATATGTTGCTAGCTCAGATTTGCAGTGACAAATTCGGTATT
ATTGTTAAAGATTTCGTCTCTCCATAATCATTCATTTAGTATGAACCTGT
TTATGATTCAGGACCAAGCAAAGTGACTTAATATTATATAATTTAGCCAA
CTGAGTAACAAATATATAAATATTTGAGCAAATTATATTGGGAGACTGAT
TTAAAGCCAACTCCTTATAAGCTTACAAGCTGTAGTTTTATTTGGATATT
GGCCAATATTGACGGTCCGGATGGATGTAGGTTCTCACATTCTTTTTTAT
CTGATAAATGAGTATTAAATGAAAATGTATGGTAGTAACTATTAAATCTG
GTCGCCAAATCTTGATTGAAGGAAGCATGAATATGTTTACATCCCTATTT
GCATGTAATACATGAATCCCTGTTGCTTTTTGATTTAGGTTGAGAAACAG
ATAAGGTATATATTGGAATCTAGTGACATGGAAAGATATTTGAAACCATA
ACTATAGAGGATGCTTGGAACAATTGAAAAATGGGAAAGCATCTGCACAA
CTCAGATAGATGACCTGACCCTTGAGTTTCAAGTTAAAAACCTTACAAAG
GGAAATGTAGTTTCTATACACTCATTCTTCCAGTAAAAATTGCTGCACAA
AAGAATTTCAGTCGTATTGTAAAAATTCCTATCAAAAACATGAAAGTCAA
TGAGAACTAAACAACATTGTGAAATCAATTACACGACTATTATTAGACAT
AGTTGACATAGTTGTATGGACTGCAACAAACTAAAACTCAATGACAGCAA
TGAAAAGCCATATCAAACTCTATTGCCTCTACTGATGTCATAACTCCTTT
CCATTAGTCGTACTAGGAGACTCAGACGTGATATAAAATATTTACTAGCT
CTCCCAATGTTCGTATCTCTTATTTTTAAGAAGATATTGGATAGATTGCC
TATAAGAACCCTCTCTCCTGAACCTTTTTATGAACATATAAATTGGTGCA
GTGGTGAAACATCTAAAGTACACTGCACATAATTAAACCCAAGAATGCTT
GACTATTATTAAAAAACTTATTGATGAAGTGCATTTTGGGGTTATTGCCA
TCTCATACTACTTTCTAATAATCTAAATGATTATCCATGTCCATTTCTGG
GGATTGAACACTCTGTGCCTGATGTAAACGTTTCCAATAATGTGCTAGTA
TTAGTGCTCTCGACAAATAGACCTTGTGTCCATTCTGATACTCTATGTTT
GAGGTGCTTAATATCATTAGTGATGATCGTAAAATCGTAAGTTTAAAAAA
TTAATTAGAGAACTTGATGAGTAATATCAAGGTCTTACTTCAAAACTCAG
TACTCAGGTTACAGTTGCCCAACTAATTGAATAAAGCTCTGAAACTCCTG
CACAGTTACTTAACATATATCAAGTAATTTCCAGCTGTAACCAATGTTTA
TATTACATACTTCTTGTGAACTTAGTTCATGTCTGTCAAATAAGAAATTT
AAACATGCACTCTATTATTGGTGAAGTATATGATTATGCACGTATACTGT
TCTTTGGATGTAAATTCAGTTAGATGAATTGGGATTAGAATAGGTGTAGT
CTAGGCATTAGACCTGTGAATTGGTTGGGCAAGTTGAACAAGTCTTTAGA
GTTCTTTATATGAAGTTATGAACATAGATTTGGATAATTAATTTTTGATA
AAGAAGTCTACATTCACCATCTCATCATCTCTATATTGCTTCCGTCAGTT
CTACATTTGGCCTAAGTTACATTATTATTGTTGAACAGGTCAGGTGGGTG
CAATTCGCTTGGGTATTAGCAGGGCATTACAGAATTGGGAGCCTGATCTA
CGTCCTCCACTCAAGGAAGGTACAAGTGCATTATCCTTTCTAGCTATTTC
TTTTCCTTTTAAAACATATCTTTGTGTAATGTGCATCTTTTTGGGGCTGG
ACATATAATTTTATGTGCTGAAGTTAGTAGGAATTTAATATGCGACTATA
GAAACTGTCCCCATGACTGATATTAGCAATTTTGAAGTATTAGATCAGGC
TCAGGATCTATTTTACATTTGTTTTTAATAATATTAGATAAATTAAATTT
TCAATTTCAATACCAAAGTTGCCTACTAGGTGCTACGTACGAGGCTGAGA
TGGCTGGGTCTTCCGAAGCTTTCTTAAATCTTCAGCCACCTAGCTCTGTA
GCACATCCTAGAATAAATTGTATATATTCTTGGGGTCTAAATTTTGAGGA
TGGAAGGCGAAGTCTGGAAATGATCGAGTGTGAGATTGCTAGCTCTAATC
CTTGTTTCATATATGTTTTTAAAATAAAGAGGCCCCTAGACTGGCCTTTG
ACTAACCACCGGAAACTTTTAATGTTTCGGCTTTAGTAGTGTAATATAAA
TTATATAATATATTAAATATATATACCTAGTGAGTGACTTTCTATTATTG
TAATTATATTTATAATTATTTGGTTTGTATAATATTAACTACACAAATAA
TCTGAAAGATATATATTGTTGTATGTTGTTCTTCAGGAATTAACTACTGT
CTACTTTTTTTAGTATAATATATTGAACTATTACTTTAACACACATGATC
TGATTACTTATAAAGGATATCTGATATTCAATCATTTATAAATTGTATCA
TTTATTGACACATATTATGTGATATAATATTCACTATCGCCATATCAGTT
GTTCACATGATTCATTTATTTTTACATCAACTTTTTGAGAATAATACTAT
AAAATGTCAGAATGAATAGCTAAAGTTATTTCTACTTCTGTGTAATATAT
GTGGCTGAAACATAAACAAGGGGATAGATCTAAATGACTTGCATTTACAG
TATATGTATATATATGATTGTAACTGTAGATGTAAATTCCATGGTTCCAA
CAGCAGAAACGTATTAAGCTTCGATACACTTTTGCATAGTCATGAAAGCC
AATATTATAATATTTTTGGTGTTTCAAGTCCTCATGGAAGCACTGCATAA
AAACTTAAGCGTTCGGAAGTTGGAACTGGTATGCTGATGGGACAAGCTTG
TTTTAGAGAACACTTGAAAAGTTTTCTTACACTTTTTGATCGGCTGGAGA
TTAATATATCTGAAGCAGATGCAACTTTTCATTCTCGTGTAGGATTGTTT
AAATTTTATAAAAAAAACGTTTACATCCTCTTAACAGTGAGTTTTCGAGC
TTCTAAGGAAGAGATGAGAAAAGAAGATAGAGGTTGAGGGGAAAAGAGCC
AAACATTTTTTTTCCTTCTTATTTTTAGTTTTTTGAGGGGTTAATAAAAG
GTAGAGATGTCAATATGATAATAATATATAAAGAAAATAGCAATGCTCCC
TTGTTGGGTGAAAAGAGAAGTTGCAAGTTAGTTATCTTTAATGGCCCACT
TAGGCGTGGGAGAAAAAAAAGATCACTTTGTTCCTCTTCTCTCCTTAAAA
ACACTCGAGACAGTTGATGTAGTTTTGTTAATTTTCTCCCTTGTTTCTCC
CAGATACACCTGTGCATAAGTTTTTTACCTTTAAAGGTCTCGTCTGGTTA
TGTTTTGGTAGTATAAAATCATATTAAATATTCTTTCGTTCTTTTAAAAT
TAATACTAATTCTTTTGCTGTGAATTTTGGAACTTGTGTTAGTGCCCAGC
CTGATAAATTTAATGCTGCATATTAGCATAATTTTAATCCATTGGTCAAG
TCTGTTGAAATAGAAAGCTGTGTTTCCTTCAAGCTCAAATTTGTTCGACA
TATTAATAATTTATCATATGCATTGGCAGCTGGGTTCTTGACAAGGGACT
CCAGAGTAGTCGAACGGAAGAAACCTGGCAAAGCGAAAGCTAGAAAGAGC
TTCCAATGGGTCAAGCGTTGATCAAATATTGCAAATAATTGATATGCCTG
TTAAAGTCTTGTGGTGGATATTTTGATGATGACTCATAAGGTGATAGCTG
ATGGCCAACAGATAAAGCAAATGACCTTTACGGAGACGATTATTAGCACC
ATTTCCAAGTATCTTCTTGATTTCCTTTTTTACGGTGGATTATATGAAAA
CTGGAAAGTTGTAGAAGCCACTGAACTTCACATCTTGTTCTTCATAATTA
TACGTAAGCATCCTTTGTTTCCTTGACATTGCAGAGAGGAACATGAAGCT
AAGAATGATATTCCTACAAATTTTGAATTGGGCTAGTTGTGTAGTTGACG
CAAGAGAATATGTTTTGAAAATCACCGAAAGAGTTTCAAACAAGTAAACC
TTGTTTTTGAAATGAGATACAGTTCGGTTATATATGTTTTGCGTAGTTGG
CGGATGAGAATGTCGCCTTTAAATAAGATTAATGCTCTTTATGCAATGAT
GAA