| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017382915.1, is a part of gene, LOC108211311. |
| The genetic_marker, MK003257 K0701, is located in gene, LOC108211311. |
| 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_017382915.1 | XM_017382915.1 | mRNA | DCARv2_Chr1:5357855..5364314 |
ATGATAAAGCAAGCCAATTTTGAGACAAGCATCTCACATTTGAGGCAAAA
TCAAAGCATGTCAATGCTCACCACTCTGCAGCTGACACCAAAACACTCAA
ATCTCCACAAAACCAAGCCTTTAACTACAATTCCATCTTGCAACACTCAC
TTCATAAATAACTTCCCATTCATATGTAACACCAAGAATGCTACATCAGC
AGCTCTGATTGGAACTGGCCTTGCAATAACAGCCCTTGTGGGCCCAGCCA
CTGCAGGAGAGTTGGCATTGATAGAGCCCTCAAATGCACTCTCCTTGCCC
ACTTGGGCCATCCATGTCTCCAGTGTTGCTGAATGGTCTTGCTTTTTCTT
GATTTTACTATTTTTTGATTGTGTGTGTGTTTTTGTTAGTTTATTGATGT
TTTGTTTGTGAAATTTCATTTTAATATAGGGTTATTGCAATGGCATTAGT
TTGGCAATATGGGGAAAAATCTGGCTATGAATCTTGGAAAGGGCTTTCTT
GGGGTATGGTGAGTTTTTACTTACTTTAATTCTTCTAAAGTTTGCATCTT
TTTTAACTTAGTGCTCAATTTGATCTTGAATTTGTGTGTTATTAGTATCG
GAATTTGTAATGATTGATTTAATTTAGTCCAGTAACCAATAGCCAGGGCC
CGGGGCGGCCATGAAGTTCAGGGTCAAAATTGGTTTATAGGGCACTAATT
TGTATATGCTTGGTCATGAATGTAGTGTGGATTGTCTGTTGTTTCTGTAT
TCTTTCTTTCCATGCATTCTCAAGTTTTTTTTTTTTTTTTTGCTAATTGA
AGCTCTACGTACTGTAAATCATTGCAGGTGCCTTTGCTTGGTGGAGCATT
CTGCGCCTGCACTTGGCATTTCTTTTATAACTCTGAGTCTCTGGAAGTAA
GTATACTGCCATATGTTCTAGTTATAGTTTGTATGTTTGGTGTACACTGT
ACATATGTCAAACAACAATGTTTTATCAGAGATTGCAGGCATAAATGTAG
TAAACTATTCATCTTTCTATGGACATGCACCTGACATTTAAATTGTACTT
GTATTTACTCCAATTTATGGCCTTATTAACTATGGATACCATTTAACAAT
TTTTAGTGTAGAAAGAGCTACGAATATAGGAATTCAGGTAGATAAGGAAG
ACTAAACAATAGCTAATTCTATTTAAGCAGCTAACATGTGTCTATAGAGT
AGTACTTGGCATAAATAATAGCTAAAGATTCTGGGTGCGAGCGGGCACAA
AAGTAGGAATAGTAAGAGTGCGAGAGGTTTAGATTAATATGAGATGGAAG
CATGTATATGTTTGTAAAGGAGGTAATGTGATTTGGGTAGGTGGAGGTTT
ATGATGATACTTGAAAGAACAGGGTTAAGTCATGGAACAAGGAGAGTGGA
AGGTTGGACCACAACGTGAAGTATACCAAGGAACGGAACCATATTGCAAG
AATTATTGACTGTTGATATCTGAAATCGTATGGTGACCATCTTCCAATTC
CTTAGTAAAGACATTAACCTGTAAAAGATTAATATATTCCTGAATTTAAG
TCTACTTTCTGCCTGTGGCATTGTTGTCGGCTCTGCTTTTTGCAGTAGTG
TGCTAAAAACGGATCATAAACCTTATTTACGAAATAAAATACATACTGCA
ATTTGGAAATTTATGTTTGCTGAGAGCCTAAACTTGCCTATGCCCAGCTG
CAGGTTGCCAGATAAAGAAATTTTAATTTATAAATACAAGTTAAATTAGA
TAAAAACAAATTAGATGAAGTTAAGTATCTAAAGAAGTGTACAGTGTAAC
TACCACTTCAGTAACTTTAGTCTGCCGTAGGGTCATTCCACAACTATATT
CAAGTCTATAAACTTTAGTCATGCCTTTAGGTTATGTTCACTTGGTGAGA
ATGAAATCGAATGAAAAAATATGAACTATTTATATGGAGAGAGTCGAATG
TTTGAGAGAATAGTGAATGAACACGTGGGAGTTCAAATTTTCTATGATGA
AGATTGTAGATTCGTAGGAAAATGGAGAATGAGAATGGAGCATTCCTTCA
AAAAGATGTGAATTAGAATTCTAGTTTAAATAGTTTGGAATGAAGGAATA
AAATTTTTGGAACATTTTCCCCAATCTCCCTCATACAAGAGTACAAAATT
CATTTTTTTCACTCCCCATTCCATTTCATCCAATTGAACACAGCCTTATA
GATATATGAAGATAAAAGTAGCAGAGTAACCTTGCAGGAGTGCAGAGTGT
GTGCATGATGCACTACACTATGCTTCAAGCTGGGCACCTTATCTTTAGAT
GATTCCATGTTTAGTGACACTATGTTGATTATATTCCCAAAGTGGGTTCC
TGGTAATCCACTCTAGACCAAAAATGGGCTTTCGAGTATAGGAGTGTTAA
GATTAATGATTATTATATGATCCTGTTAAGTTCTCCTCCCAAGTTGAGGT
TTTAGGAGAGTAGTTTGCTTTACTTAACATACCAATTCTTCAGCTACTTG
GAAAGCTCGTGAGTTTGATGCAAAGCACAGAATTAGTATAAATCAATTAA
CATTAGTTTTCTTTCCATTAGGATTTTATACCTTTGTCTAACTAGTAACC
AGCAGACCAGATATAACTAATCCATACACTCTTTTCTGTTGATGGTCGCC
ACTCAGTGCCCATGTTACTTGCATCTCCCGGCTTAGCAGTCTTGCATCAT
ATATTTGTCAGACCTCCAAGTTGTAGCAAATTTGTGTGAATTACTTGCTA
TCAAAGTCCTGTAGCAAATTTGTGTGAATTACTTGCTATTAAAGCCCTGT
TCAACTGTAAAGAGCTGATATGTACCATGAGTAATGCACATTTTTACTGT
ACATATGTAAAATTTCTATGAATACTCATATAGAAATTTGTTTATTTACA
ATCTATAGCATCATAACCTTGTGGAGCTCCCCCTCCCCTCCCTAAAAAAA
TAAAAGAAAAGAAAAATCCCGACTGTAAAAGTTGTCAGATAGACATCTTA
TTGATTAGGGTCTCTATGAACAGGTGCTTGTAGCTCTTCAAGCTGTATTA
ACAGTTATCGGCAACGGAACAATGTGCATTGCAGCATACCGTATATTTAA
GTCAACAAAGGGAGGTGAAGAGAAAGCGTGATGAATATCTTGCTTGCCCA
AATGAGTCGACTCTCGTCTAAACAGTAAATCATATTATCCTTTACCACTG
ATTGAGATAAAGTTTTTGTATGTGTCCTGTGAATAGAAAAGCAACAGATA
TGGCAATTTTCTGTTGTATCTAAATAAGTAACAAACAAATATTTGATCAC
ATTGAAAACTGCATTATCTTGATACAGTCATTAATTTGGATATGCAGGAT
GATGCGGAAGTTGGAACAAGTAACTAAAAGATTACTTTGTATCTTATGTA
ATTATATACGAACTAATTTATTGTAATTCATATAAAGTTTAATTTATTTG
ATCATCAAAGTAATAGGAATGCTATAGGTTATGGGTAATGGAGTAATAAA
GGAGTTGTTAGCTATGGTGTTTCATGCCTTCCTTGTCCTCCATAACAGGA
AATTCCTGATATTAAAAATGAAGCCCTCAGATATTTTTTGGATGATGTTC
ACAATCTGTGCAGCCTAATTTCCAGTGTAGATAGAGCTTTTCCGTAGGTA
AAGAAATTCATTATATACTACATTTTTCTTTTACTGGTCCATTTTTCATC
CATGTTGGTTGCTCTTGATCCTATATAGTATATTAGCATGTTATTCTTAC
AAAAATGTCTTGTGCTTACCATCAGCCTATGCCAAATTTATGAACTACTT
TATATATAGTAGTTTTTGTAAGTACGCTATGTATCCTTAGACTGCAACCT
TCATGTTATTTATTCGTGGAGGTTGTCCATGACGCGCAACAAGATCAAGG
CATTGCATGCTACCAATTGCAGTCTATTCCTACAATACTCAGCCAGAAAT
ATGCGTGCTTGTTTGTCATAATTAACTTGACAAGTTTGAAGCCTGAGTTA
AAGTACTTCAGTTATTTATACATCTTCAAATAGTTTGGATAACAATTTTC
TTTTATACTTATTGAACTTAGCTCATTTAGATATTACCCATAATAGATAG
TTTGCTTTCGAAAGTCATCTTCAAGACCAGATATGATCTCCTCTTCTAAA
CAAGCTAGTGCAAGCTACAAACTAAGTTCTGGTAGTAATATTAATATATA
GTTTTAACTGTTAAACATCTCAAAACCTCATCAGCATAACATGAGGTTAT
AATCTATATTCCTTCTAAATTAGTTTAAATAGTCATGGAATTAGGAACTA
CTACACTTGTATTTTTTCATCTTACCGTATACTAACCAATTAAGGTTAAT
ATTTGAAGCAAATCATATTAGTATTATTCTGTGATGAATATCATAATTGC
ACTCCTTATAAATGCTTTTGGTAGAAAAATTAAATCAAATATCCATCTTC
CTTTTATATGACCTATAGATTTCAAGAGTTATGTTAAAGAAGAATTCCCC
GCGCAGTTGTTAGCATCTGAGTAATTAATGGTTGGATCAACTGGTCCATG
GGGATTAGATGTAGTCTCATTAGACTCTGACATGGTGGTCTCTTTGGAAG
ACATATTCTCATAAGAAACAAACAATTATTTAGACATGGTTGAGAAGAAA
ACAATATTATAATAATTAATTCTAAATTATTGATTTATAAAATTAATCTA
CCCCACAATCAAATTAATGCTATTCTTTACCCTATTTACCCCATTATAAT
ACATATATGTAATGTAAACAAATGTTATATAATGAAGCCAGTTTTGGACG
AACTATATACTATGTTGCAGTGACTGTATTTTTGTATATGTCTTGATGCT
TCCTAGCTAACCATTGCTGATATGTAGTGAAGTTTCAGTGAAGATGGAGT
AGACATACATGCATCTATATAGCTGTGCTGCAGTCTAAGAAATTTATCAT
GTCCAGTGATAATATGAGTAATCAACTAACAAGCTACAATAGCGTAAACA
AATAACATAATGGATAGTTACTTTAAAATACTACGACACTAGTAACAAAA
CTAATGAATAGCTACTTATATTTGTTAATTAGCACAATTAGTGCATTTTA
TATTTGAGCAAGGACTTGTATTAAATCTCTTAAATCATCAAAACAACTTA
GAAAGACTATTGGGATCAAGAGATGTGAGTTTATTAGTGTATGATGTGTC
TACGGATTACAGAAGAGAAATTATTTAAACAAGGAAGGTGGTTACTTTAA
ACAACACATTCTGAAAAAATAACTAGAGTTATGCCTTTGTCAAAGACTAG
TGAGTCTTGTAGAGCTCTAGAGCTCTCAATATTATTTGATACTCTTAAAA
GGATGTACACGACAGAATATGTGGTAGTACTCCTCCACTGCGACTTCCAC
AATGAACTACGGCTCTGCACCTTGATCTCTTCCCACCCATTAAAGTACAT
CTTCTTATTAAGATTAACATTAATTATTGAATAGCAGCTTGATGAGTAGA
TCAATAATAATAATGCAAAGCAATGAAACGATTCTAGCTAGGGACTCAGT
CTTGGTGGTAAGTTGGGGAATTTAGGGTGGAGGATACGCATTGGTGCTGA
TGAGAGGGTTTTTTCTTCTGAAACTCAGACATCAAGCTTAGGTTTTCTTG
GTGTAGAAGACTAGCTTTCATTCTCAGCTTCTCATTCTCATGAAAGATAG
TAATGTTCTCCATGTACAGCTTCAAGTTCTTCTCTTTCATATCATCTCTA
CTTCTCTTTCTCCTGTCATATATCATGCATAATGCTTCCATGCATCAATA
AAGTCCGGTTTAATCTTATTACCATATAAAGTATATAATACAATTAAATG
TTTACATGCAGATACCTAAATAACATACCTGTTAAGCCTATGAACTTGAA
TCCTGTATCTTTTGGATCTTGCTTTTCTTTTGTACAAAGAGAAGGACGAC
GAAGTCCATCCGGAGGAGGTACTTCCGATACACATCTTCCCAGTTTTTAA
AGCTGTTTTGCGCTTCCCATCGTTCAATTTTATCGAATAGGAAGTATATA
TTACAAGGATTGAGTAGAATTAGAACTTGTAGAGGGATTGGTATAAATAG
CTGAATGTTATGGTTAGTTATGGGTGAATGTGGTATATTACATGGTGGCC
TGTAGGCTCTGAGAGAGAGGGAGAGGAGATTGTTAGATTCAAGAAGTGTA
ATGATGAAGGGGAGTCATGATTACAAGAGAAGAAACCCCCATGCATATCC
ATCCAGAAGAAGCCCAAGGGAATGTATTGCTGCCTTCTAACCATCTCTGT
CAATATTTTCTTATTGCAAGTCACAGGGTCTAGTATTCTTCTGTAAATTA
ATCAATACACACACTGATACTCTTCTTTCATAGTTTACACTTACCCCTGA
CACTTTGGTGTTTTTACAATATTTCACCCCCTTTATGTATTTCTTTAAGT
ACTTCCAAA