| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017387959.1, is a part of gene, LOC108215451. |
| The genetic_marker, MK006610 K4054, is located in gene, LOC108215451. |
| 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_017387959.1 | XM_017387959.1 | mRNA | DCARv2_Chr3:31622375..31628116 |
CATAAAATTCGTACACACACAACTTTAACCTAGAAGGAACTACTATTCTC
CAGTCGCTAGCAACACAACATCACTCTCCTTCTCCAGTAGCTTTCGCTTC
CCTTGCTTCATCCTTTGATTTTAAAGGTACAATCTTTATCAGCAAAATCC
AATTTCTTTATTCAATTATTCGTTGCTTCATAGATTATTGCATTTCTCCT
CTGTTTCTTTTATTTCATTTCACTGTTTTTTTCAATGTGTTGCACCTCTT
CTTGGTCCGTGATCAATGCTTTAGTTAATCTTCGTTCTTCTGTTTAAAGG
GGGTTTTGTTCACCAAGATTTATGCTTTTAGATCCGGGGTTTTATGGGAA
TTATCTAATTTTGATTTTGTTGATTAAAAATTGACTCTTTATTTGAGTTA
CTCAGGGTAATGCTTAGGGGTTTCATTTCCCTTACTTAAAATGTGTGTAT
GTGTACATATGGGTATATGTTATGCATTTCAGATATCATTTAAAGGTCAG
AATATGTGGCCCAGTACGTTGTTATGGCCTTGATTATGTTTTCGGTATTC
AAGGAAATCGTCTCTGTATTTATGTGTTTCAGTGAATTTCCGTAAATTTT
AAGATCAAAAAAATGTACATGACTCATGGTTCAGTAAATTGTTATGTTCT
TGCTTTTTTGTTAGATACTTGGGAAATTATATGTGTTTTAGTGTTTACAT
GTTGCTGTATTTTCTTCTTCGTTGCTCCGTGTATAAACATAGTTATTGAA
TTTAGAAATTCAAGATGTTTAACAATTACAGGTTTACTAAATTCCAATGC
TCTTGCTTATGTGTTAGACATTTAAGAAACCATCTCTGCTTTATCATTTT
TTACAGGGCTGTTGTTTTTTGTGCTCTTCCTTTGTGGTCAAACATAATGT
GGCATATGTTGACTTTTAGTTTTATACCGCACTTGGTGAAATATAACAAT
GTCTAGGTTTTTTAACGTTTGGAAGAGTATTATACTTGTAAGTTATACTG
TAATAATCTTATATGGAGGCATAATTTAGGGCTATTAGCTATACATGTGA
GAATGGACTATTTATTCAGAAGAATACTTTTTTGTTATATAATCCAGAGT
GAAGAATCTTTATGTTGCTACTTGCTACCACTTTCAGTACCTGTTTGCTT
CTTTATTTTCATTGTCTAAAATTATCTTTCAGAAAAAACATAAGTAGCTT
AATAATGATATGTTGTTGCTGATTTTCAGAGTGCAATGACAACCCAAAAT
GACATCCCTCCTGTTCCTAGTGCGCACAATGTTGGCATGGCTTTTGTCGC
ACAATACTACCCCATTCTCCAAGAACATCCGGAATCGGTTTATAAATTTT
ATCAAGATTTAAGCGTAATAAGCCGGCCAGAACCTGATGGTGGTATGATA
TCAGTGACAACCATGAAAGTGAGTCTATGATTTGTAGATGCTTTTATTTT
TGCTATAGCTCTGTTTTTTCACTAGTTGTCTGGGTTTGCTTGTTTCGCTA
GTTGAACTCTCTCTGGCATTTAATACTCTATCACCTGCTCATGTCATGTT
CACCAGTAGACTTGTGTTTTAATACCACAGCTTATCATTTATGTATCAGA
ACTTCCAAAAAAAAATTACCTCTCGGGGTACTGTTTGTACCTTGTTTATG
ACTTAGCAACCACACTTTAGAAGAAAAAGTCTAATATCCAATGTGTAACC
TCCCTTGAATTTCTTTTGCTCCTTCCTTTCATAGTTGGACTTGGGGTAAT
GAGTATTCACTCACTCCCTTTTCAACATCATAATTTGACTTCCAAAATAG
TAAAATACCATTGTTCTTTAGTTTAACAGTCAGATATTGTCTGTGGAACA
GGATATTAATGACAAGATATGTTCTATGAATTACAAGACAGCAGAGATAT
TGACTGCAGATGCACAGGATTCAATGAAAGATGGAGTGATTCTTCTGGTT
ACTGGATTCTTAACTGGTGCAGACAACCTACGAAGAAGATTCACACAAAC
ATTTTTTCTTGCTCCACAGCATGTAGGTTACTTTGTTCTCAATGATGTTC
TCAGGTACATTGATGAAAATGATCCTTTAGATGCTAACACAATTTCGGTT
AGTGGGATTGATGACACCCCATCAGCCAGCCTGACACCAGATCCAGGTTG
ACTTGAAGACTTTAATTTCCATTGTTTAGAGTTATACTGATATTTCTTTT
AATGAATTTGGATACTGATTCCAATTTTGCTTCCAGAGCCATCACATGTG
CTTGATCCTCCAGTATTAAACCAGGAGAAGTCCCAAGTTGAGGAGCTTCC
AAGTATTGAGATAAAGACTGCTGACCCAAAAGGAAATGAGAGTGAGTTGG
TGAGTACAAAAGCTGCTCCATCTTCTGAATCTCACCCCATAGAGAATCAT
ATTTCAGCAGCTCTAGACACAGCTTCTTGTGATGCTGAAGAGGATGCTCC
AAAGAAGTCATATGCGTCCATTGTAAGTTCTCACACAAAGAAGGGAATCT
CAGGAACTGTTAAGATGTATGTGCCTACTAATACCGCAAAGGTTGATTCT
CCGAAGATTGAAAAGCCTCCTGTCAAGTCTATCTCACAAGAGCCAGCTCC
AGCTGCTTCAGTTCCTAATGTTCCAGCAAGTAACCATGCAGATGATGAGG
GTATATACATTTCTTTTTATTAATTAATTATATAGATTTTGGAATTATTA
ATTAACAATATAAGGAAAATTCTGGGAGCGAGAAATGATATTCATGTTTT
CTTTTTTTCTTTTTTTCTTTTTTTGCTTTTTACTAAATTGAAAGCATGTC
AGAGTAGAATCCAGTTTGTTGCAATCATTGCAACTAACATGGTGACTATG
GATAGAACTCTTCTCCACATCGCAGCCTATATCTTTTTGACATTGTATTG
AAGTTATCTACTTCATATAGGTGACGGCCACTCTATCTATGTGAAGAATT
TGCCTCTAAGCGTAACCCCCAATCAGCTTGAGATGGAGTTTAAGAGATTT
GGGCCAATTAAACATGGTGGAGTTCAAGTAAGAAGTAACAAGGTAATTCT
AACACACTGAACATGTATGTTGTTTTCTGCCACATGAAGCAGCTGCTCTG
TACATGCTTATTTTCTTTTGGCAACAGGGATTTCGCTTTGGCTTTGTGGA
ATTTCAAGATGTGAATTCTATGAACAATGCAATTCAGGTGTGTTCTATAA
TAACCCTTTTTATAGAAGGAAAATTCAGAAACGATATGATGTCTTCTGTT
GATATTTAAAAGGATGTTTTAAGCTACCGAGGTTCGCTTTGTGTGGAAGA
GCTATTGATTTCTGATATGATAAGGGAATATTAAGTTAACATGTTTGCCA
TTTGAGGCCTTACACCGTTGAACTGATAGATAGTGTGTTACAAAAGGCAA
CCCAAGGGCAAGTTTAAACTCTGTCAAAATGCTTAAGTAGTTATATTACT
AAAGTCTAAACATATGTTTCTAAGAGTTATAACTAATATCTGATCAAATG
TGCTCAGGTAAGTGCTGTATACTATAGACATATGCTGGTGATTTAGCAGT
CACCTTATAAACAGTTCAGTTATCCAAATATATTCATGTATGCATTGTGA
CCTTACTAGTTACTGGTGAAGAAATTATCATGAACACTTATTATCTTCTC
TGCTTATTTGTCCGGGTAAATATAAGAACCAGCTCATTTATTATTATAAT
TCAAACTTTTATAGTCATTTAGTGGCATGCTACAAGAACATAAACCCTAG
TTTTCTCTTAGACATTGCCTCTTGCTTATAACTAAAAGAAATGAACATGA
TCATGAACTCCTGATTACCAAGAAGTGAACATGATCATGAACTCCTTATT
TCCTCTCTTTGTGACATTTGGGGTCACGAGCCACAATCTTTTTTTGGTTA
AGAATTAAGATCAATTTCAGGATTTTAATACCCACACACACATGCCTCTG
CTAAACTTAGATCCCTTGACCTCTTTCTAATTGAGAGGGATAGCTGCTAG
GCTAACACTTTGCAGCTACATTATTCTTTTGTATTGTGTATCAACAGACT
GATAGACTTTATATATACTCTAAAGAAAACTAGATTGGAAGCTTCAATAC
TTGCAACTTGCAAGTGCTAAAGTTCAAATTTCAAATATGACAGATATATA
TTTAGCCCTCAAATTATTCATATCAAGTACAGTTACATTTTGAATAATTT
TATCACTGTGTCTGTATTAGCTTAATTTATCCTCTCTTTTTCTGAATAAC
CTAGAGGTTCTTTTTACTTGACAATTTATCCAGAAGCCAATTTTAGCAAA
CAAAGCATAGGTTCTCTTAGAAAAAGCCTGCTTAACTTGTGATCTGTAGA
AATTTTTACATAATATAAGCGTTTTCCCTAGAAGCTAGGTCTAACCTTTA
TTACCCATCTTACTGTTATTAGTAAAAAACGGAGATAACAGAAATACAAC
TTTGTTTGCATGAGAACATAAAAGTTCTAAGGATGGATATATCGTCGTCT
GTTTACCCGAGCTTCTTAACTCTTTTCTAACTGCTAATTTAGCACTGTTT
TACTTGTAGCCATATAAACTTATTTGACTGTTCAGCTGGAATACTGTTCC
TCATCCGGAAAGAATACAATGAAAGTATTTCATAGGACTTGATTATTTGT
AAACAAAAGAAACTGTCATTCTTGTCAACTCAAGTAGTCAAGTTGTATCA
ACATGACCAATATACAGTTGCTCTAGATCCTAATTTCTTTTGCCAAAGTT
TATATTATCCTGTCAGGGGCATGTGTTGTGAAATGTTCGAGCTACATTAT
TGAAAACTGATAATAGCATATACCATGCAGATAATATGCATGTTTCCCCT
TTTAATTTTTACACTTGTTTAGACACTCTCTTTGCAACCTAAGACTGGTT
CAATTGCTTAAACTTTGAAGTATTCTAAATATAGACTATTACCTTCTAGG
CTTCACCAGTTACAATTGGGGATCGTCAAGCAACTGTTGAGATAAAGAGA
ACGACTACTCGAGGTAAGAAATTGTGTTAATAGTTTTTTGTGGATATGAA
GTAACAAAAATTGGTGACGATGAAGTACTCAAGTAGTTGCAGATGATAAT
TTCGGCTCTATTCATTTAGCTAGATAGGTTTGTGGATAGTTCTAATTTTA
TTGTATTTTGTATCAAGTATCTGATATAGCTGGTCTGTTGCTACCTCTTG
CAGTGGGAAATGCAGGGAGCAACTCCCGTGGTCGTTTCTCTTCTGGACGA
GGAGGGTACAGGAATGACAGCTTCAGAGGCCGTGGAAATTACAGTGGTGG
AAGGGGTTATGGCAGAAATGACTTTGGTGGTCGTGGTGAATATTCTGGGC
GTGGAAGGGGTCCAGGTGGTCGCAATGGAGATGGAAACCAGCAAGGAAGG
GGACGAGGGGGCCGTCGAAGTGGCCCGAGTCAAAATGTAGTTGCGTCTTA
GAAATTATGGGTTAGTTATTTAGGACAGTTTTATAAAGAAAATTATATGA
GCAATGCAGATGTGAGCACTACAAAAGTTCATGGTAAGTTATTTAGTGAT
GTCAGAAACTGTACAACTTCATTGATTTCAATATGAAGTTCGACTTCAAA
ACACAAATTAGTAAGAACATGGGATGTAGTTTTCAGGTATTATTTCCTAA
CAAAATTTTGTTTAGGTGGTTGCCTTTCTTTAATAGGAATAGAATGTAGT
TTTGCAGGATTCTTATATCAAATTTCCTTAATTTTTTAAAA