| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017367819.1, is a part of gene, LOC108199827. |
| The genetic_marker, MK006320 K3764, is located in gene, LOC108199827. |
| 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_017367819.1 | XM_017367819.1 | mRNA | DCARv2_Chr8:29506281..29512644 |
ATTCTAGAGTGAGAGGAGAGAAAAAAGTAGAGAGAGTCAGACGGAGAGTG
TTTCTTTTGTCACCCTACACTTTCTTCAAATTTCCCGCAAATTTCTTAAA
GACCACCATCACTTTTAGTAAATTTTGAACTCTGCATTCATTTATTTTCT
TCAACTACTCTTAGTACAATAATACTCCCATTTTCTATACACATATATTA
ATATTTTTCAAATTGTTTTTGCCTGTACAAATCTCAAGATTTGATATCCA
GATTGTCAGTTTCATTTCTGCTTGGTTTCTTGTTGAAAAGTAGGTAAATC
TTGAAAAACTTACCTTCAAACATTGCTTGTGAACCTATTAATGTGCATTT
TGCAATGCACATGATTGCATTTCATGTGTGCTTTAGCTTTTTCGAGATTA
AAATATTTAATAAACTAGATTATTCGATTCTTCCATCTTTTTGTGATTTT
TTCTAGTTGTTCTCATGAAACCAAAGTGTTATTGGCCAAATATACTATAC
AATGTGTGAGTGTGTCTATGAATAGATCTTTTCCCTTTTTCATACAATTT
TGAGTTCTTTAAGTTCCTTTCATTTCTTGATTTGATTGGTTTCTTTTTAA
AGAGCTTCTTGAATTTCTTGGGCAAAGATCAAATCTTTTTCATAATTTTG
AGGTGGGCCAGTGTAAAGATTCAATCTTTCTCATGATTTGAGGTGGGATT
CTTGAGAACTTGTGTTTTGAGGAGTTGGGTTAGTTTTGAAGTTGGATAAT
TGTGAAAAAATGCCTGGTAGAAGGAAGAAGATTCGTTTTAGCAAGATCTA
TACATTCAAGTGTAAAACAGCAGCTGCAAAAGATGATCATCTTCACATTG
GTGGACCTGGATTCTCAAGGGTAGTGTTTTGCAATGAACCTGCTAGCTTT
GAGGCTACAAGCAGGAATTATGCAGATAATTATGTTAAAACCACAAAATA
TAGTCCTGCAACTTTTGTGCCAAAGTCTTTGTTTGAACAATTCAGGAGGG
TTGCCAATTTTTTCTTTCTTGTTACTGCTATTGTGTCATTCACCCCCATT
GCGCCGTATTCTGCTGCTAGTTCCATTCTGCCTCTGTCTATTGTGATTGG
GGCAACCATGTTGAAAGAAGGTGTTGAAGATTATCGACGAAAGAAGCAGG
TAGAAATGCCAATTACAATTCCATTAGTGTTCATGGCTTAAGCTAATTTA
TCTGGTTTTCGGTCTGGATTTTTTGTTGGATTAGTATGTTGAGATTTATA
TGGTTTTCGGTTTTTGTTTGCTGATTGGTAGCACTTAGATCAGAATATGT
GGTTTTATTTGAGTCAGTCATTTAAACCATGTTTTAGTCCAGAGTATTTT
TCTTTTCCAGCTCTGGAGTTGGTTGATTATGTCTTAGAGATTATATATCT
GTTTGAATTATGGAAATTTAAGGAGCTTTCACAAATCACAATATTTTGTG
ATAAAAGATCTGCAATTCTGCATAGTACTTCTAATATGCCTTAAATTTTG
ATTTCAGATCCTTTGTACGACTAGTGGTTTTAGTTAGACTTATGAACTTC
CCAATAAATTAGATCAAGGACATTAATAATTTGGCGTTGAACCAGAGATT
TGATTTTGCTTACCTGATCGTATTTGTAAAGATTTAAGCGAACATACACA
TTAGTACTCTTATATACTTTCTCCATAGCTAAATGTCAACTTGGCATTAT
TACTGAATGTATGGAGATCTCTTTCAGGATGATGAGGTGAATGGCAGAAA
AGTTAACATGCATCAGGGTGATGGATCCTTTAAACTGTGTATATGGAAAG
AACTGAGAGTAGGTGATGTAGTTAAGGTTCAGAAGGATGAATTCTTTCCG
GCTGACCTTCTCTTGCTTTCATCTAGTTATGATGATGCAATCTGCTATGT
TGAGACCATGAACCTTGATGGAGAAACAAATTTGAAGCTAAAACAATCTC
CAGAGGTAACCTCATCCCTTCACGAGGACTCAAGCTATAAGAACTTTAAG
GCCACCATTAAATGTGAAGATCCAAATGCAAGTTTGTACACTTTTGTTGG
AAGTATGGAGGTGGAAGAAGAAAAAGTTCCCCTTTCTCCACAACAGCTTC
TCCTTAGAGACTCTAAACTTAGAAATACAGAATTCGTATATGGAGCTGTT
GTCTTCACTGGCCATGAGACAAAGGTGATTCAAAACTCTACTGCACCCCC
TTCGAAGAGAAGCAATATTGAGAGGAAAATGGACAAAATTATATACTTTC
TTTTTGGCGTCTTGTTCCTAATAGCATCTGTTGGATCAATTGTGTTTGGA
ATTGTAACTAAAGATGACCTCCATGGTGACCGCATGAAGAGGTGGTACCT
AAGACCTGATAAAGCTGAAATATTTTTTGATCCTGAACGAGCTCCAGAGG
CTGCAATGTATCACTTCCTAACTGCCATATTGCTTTATACTTACTTGATT
CCAATTTCCTTGTATGTGTCAATAGAAGTTGTCAAAGTTCTTCAGTGCGT
TTTTATCAATCAAGATATTGATATGTACCATGAAGAAACAGATAAACCAG
CTTATGCCCGCACCTCAAATTTAAACGAGGAACTTGGTCAAATTCACACC
ATACTTTCAGACAAGACAGGAACACTAACTTGCAATTCAATGGAATTCAT
CAAGTGCTCTATCGCAGGAACGGCTTATGGTCGTGGTGTCACTGAAGTTG
AAAGGGCTATGGCCAAAAGGTTAGGATCTCCGCTGGATGGAATTAAGGAT
CAGAAGAAGGATATGGAAAATAAAAATACAAAACCCCGCATCAAAGGCTT
CAATTTTGAAGATGAAAGGATCATGAATGGGAACTGGGTTCGTGAACCTC
ATCCACTAATCATACAGGGGTTCTTGCGTTTGTTGGCTATTTGCCACACT
GCAATTCCTGATAAAGATGAAGATACTGGGAATGTCACGTATGAAGCTGA
GTCACCAGATGAAGCAGCATTTGTCATTGCAGCATTACAACTTGGCTTTG
AATTTTATCAAAGGACTCAAACTACCGTTTCATTGATTGAGTTGGATCCT
GACACTCATGAAAAAGTTCAAAGGTCAGTACACAGTGTTTCAAATTTATG
GTTTCCTTTTTATGCACAAATCAGTTAGCTAAGGATTTTATTAAGGTGTT
TTCACATTAAAAAAAATCACATTGAAAATTTTACTTTGGCAACTTCCTTT
GCAGGGATTATGACATTTTGAACGTGTTGGAATTTAACAGTACAAGAAAG
AGGATGTCTGTTATTTTGAAATATGAGGGAAAATTTTTGCTGCTCTGCAA
AGGTGCTGACAGGTTGGTCAAACATACTGCTTATATCTAACCAAGACAGA
ATTTTCTCTCTTTGACATATTTTATGTGGTACTTTGAGTCATCAATCTCG
GTCCTTTTAACTTTCCTTTCTAATACTTTGTTTTTGGGTGTCTTGCTAGT
GTCATGTTTGAAAGACTTGGAAAAAATGGAAGGGAATTCGAAGAAATTAC
CAGAGAGCATGTGGATGAGTATGCTGATGCAGGTTTAAGAACATTGATAC
TTGCTTATCGTGAACTGACTGAAGAAGAATACAAAGATTTTAATGAGAAA
TTCAAAGCGGCAGCGAATGCAGTTAGTGAAGATCGAGATACTATGATCAA
TGAAGCCACAGAGCTGGTTGAGAAAGACTTGGTCCTTATAGGTGCAACAG
CAGTTGAGGACAAACTCCAACAAGGGGTGAGCTGAAAAGATACTTTTGCA
GAGAATACATAAATGTTACTTAACTTCTTTAATGACCAAGATTTTTAATA
GATATCTCCTCTCCTGTCTGGCAGGTCCCTGAATGTATTGACAAGCTTGC
TCAGGCAGGAATCAAGATATGGGTTTTGACCGGAGATAAAATGGAGACTG
CAATTAATATCGGGTACAGAACTTTTTCTTTTTTTTAGTTGTGACAATAC
ATATAACATGAAGTCTACTCGCAATACTTTCTAATTTATAGGATATATAC
GCTTCAGGTTTGCTTGCAGTTTACTTAGACAAGGAATGAAGCAGATAACA
ATAACCTTGGAAACACCAGAGATTAAACAATTAGAGAAAGTGGGAGAAAA
AGGTCCTATTGCTCAGGTATGATTCATTTGAGTTATGTTCTAAAGTGACA
GTTTTAAATAAGGATCCCATTAGATGTTCAAAAGACCATATGAACCGGAG
AAAAATTAAACAGAGAGTCTTCAATTTTCCTCAACTTCTAATTTTTTAAG
AATCTTGTTTCTGATACCATTTAGTGTCTTTCATGAATTTAAATGTTGCG
ATATTGATGTAATACGTGCATCTCTCTTTAGGCGTCAAAGAAAAGTGTCA
TGCAGCAGATAAGTGAAGGAAAGGATCTGATTGCCTCATCAAAAAATGAG
GCATTTGCTTTGATCATCGATGGTAAATCACTTGCATATGCTCTGGAAGA
TGACCTGAAAAAAATGTTTTTAGATCTAGCAGTTGAATGTTCCTCTGTTA
TTTGTTGTCGCTCATCACCTAAACAGAAGGCACTGGTGAGTTTTCAGCTT
TATAAGAAGTACTTAGTTTCACAGAATACTTAAAGCAATTTACAAGCAAA
TCAAGTTTACTTTTTACTTAAAGTCCAGTTCTAAAAATAAATTTCAGGTA
ACTAGACTTGTTAAGGAAGAAACTAAAAAGACAACACTGGCAATTGGTGA
TGGGGCTAATGACGTGGGAATGCTTCAAGAAGCTGATATTGGCATTGGGA
TCAGTGGTGTTGAAGGAATGCAGGTGCTTAATTAGTAGCGACATATGATT
GTCGTTCTATTTTACCTTTCATATGATTTCTTCTGTACCCATAATATATC
TTTCCATATTTCAGGCGGTCATGTCAAGCGATATTGCCATAGCTCAGTTT
AAATATTTGGAGCGCTTACTGCTGGTGCATGGGCATTGGTGTTACAGAAG
GATCTCTTCTATGGTAATGACAATTATGGTGTTGATACAGTTGCTGATAT
CTCCAACATGCAATACTGAGTAAAAACCTACTCTTTTTGCAGATATGCTA
CTTTTTCTATAAAAATATTACATTTGGTTTCACTCTCTTCTGCTATGAGG
CATATACCACATTCTCAGGGCAAGCTGCATACAATGATTGGTTTTTGTCC
CTTTACAATGTGTTCTTTACATCACTTCCGGTGCTTGCATTGGGCGTTTT
TGACCAGGATGTATCAGCCAGATTTTGTCTCAAGGTATGCTTTCCACAGG
TGGAAAAATGTATGTCGAGTGTCTCTGCATACATTTTAATATTTAACTGG
TGGAAACGTCTCTGGAAACAATCCGCAGTTTTGGAAAGTGATTGATTTCT
AATATACGTTTGTTTTTCTTTACAGTTCCCTTTACTGTATCAAGAAGGTG
TGCAAAATGTTCTTTTTAGCTGGCGAAGAATAATTGGCTGGATGTTCAAC
GGAGTCTGCACTGCTATTATAATCTTCTTTCTCTGCATTAGAGCACTAGA
ACCTCAAGCCTTCAAGAAAGATGGGAAGACTGCCGATATGGATGTGATGG
GGCCTACGCTTTATACATGTGTAGTCTGGGTAGTTAACTGCCAAATGGCT
GTTTCTATCAGTTACTTCACCTTGATCCAACATATATTCATCTGGGGTGG
AATTTGTCTCTGGTATTTTTTCCTCCTGGCATACGGGGCCTTGTCTCCCA
CCATTTCAACTACTGCGTATAAAGTCTTCATTGAAGCCCTTGCTCCATCA
GCTTCCTACTGGCTGATCACCCTTTGTGTCGTGATCGCTGCCCTCACTCC
TTACTTCTCATACAAATCACTTCAGATGCAGTTCTTCCCTATGTACCACG
GGATGATCCAGTGGATAAGACATGACGGGCAATCAGAGGACACCGAATAC
TGCAATTTGGTTAGACAAAGATCAATAAGGCATACGACAGTTGGCATCAT
GGCGCGGTCTTTGGCAAGAACTAATCCCTTAACTGGCAGTACTCACAGAC
GCAGATGAACATCAAGATTTTACACCATGCATTACGGTTATTGAACAGAA
TCTTTACCCCTAGCGCGTGATAAACAGATGGGCTGTTATTCCATATATAT
TACAAGTTCTGAAATCTGTACAGCATCATAATTGTACATCATGTAAGGTT
GTCAGATAGAGTTCCTGAGATTTGTAATTTAATTAAGTTTTTTTTTGTTG
TGTTTTTTTGGTAGGAGTACTACTAAACCAAACATCTCTATGTTGAAAAT
TGTTAAAGTCTTGTTTGTAGAGTACAGGTTCATCAAGCTTCTCTATTCAT
TTGTAACCAGACTCTGCTGTATAACAGATTCTGATTGAGACAGTAAATAG
CAATTTGTAAGAA