| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017387677.1, is a part of gene, LOC108215260. |
| The genetic_marker, MK003346 K0790, is located in gene, LOC108215260. |
| 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_017387677.1 | XM_017387677.1 | mRNA | DCARv2_Chr3:21605008..21611826 |
CGAAATCATTCACCCCAACCAAACACAACATAAGTACTCAAACTCAACTC
ACACTCTCTGAATCATATAAGATATAAGGTGCTGCTATTTTGCCAAAGGC
TCTCATCACTCCTGGACGTGCTCTTGATTCACTCATGTGCTTCTTTCCAG
TTCTTGATAAGGTGAAGTAACCGAGTCCACAAAATATGTTTTTCTCAATC
ATTTGCATGTGTAGTGTTAGAGTTCTCAATCATCTACTTAACATAGTAGC
TACTTTGTTTAGTTTTAATTGCTTTTGTTTAGTTAGCTTTGATCAACTTA
TTAGTTGCTTCTGCCATCAAATTTATGACCTCGGTTCTTAAGTTTTATGT
TACTTTAAGTTAATTAGTTGCTCTGATTTGTTGTTATCTTTTCTGCTGGG
TTGTGAAATAGAAAAGGGGATTTGTTGAATCAATTGATTATTATCTATTC
CTAGAATTTGAGTTTGTTGGTAACTTAACAAGGTTCAGGGAGAGATCTCG
ATTTCGAGCCCTTCCACCCCAATATTTAAATTTATTTGTTATATTTTTGG
GTATTTAAATCAAAAGTGGGAGCTTTAATTAATAAATGTTATTTGTAACT
GTTCGTATTCATCCTTATATACTGTTTTGAAAAATTGGTATGTAGGACTT
TCAAATGTTGTTCATACTTGTGGACCAATAACTATAGCTACTTGGATAGG
AAGAGGAAAAAACACGCTGAGAGGCAACAAAAATTTACCAGACAGCATAC
AATCTGTTATAAATTTGATATAGTTATATTACATATTGTTTAGTACTGGC
AAGTGGCAACAAGAACTATGCAAGAAGTTTGTATTAATCATTTAATTTTA
TTACTATTTAGTTTATCTTAGTCTCTTAGATTATTAATTTACACTAATCT
CACATTACAATTACCTGTAGAGGTATCGATTTGTACATATGCGTGGTTAT
ATATCAACATAAAAGATTGTCATTTTTGAAATTTGTAATATTTATTTTCA
CATCTAAGGAAAGAAAAATTATTCTGTTCACTGATTTTCATATATTAACT
CTCTATATTTCATCTTTGGTGCAGAATGATATGTAAGATATAGTTAAGCA
TGTTGGCTCTGAAAATGAGCTAATTATTATACTTTATAAATTTCTTTTGT
GTGTCAGTTAGTGTTAGAGTTCACTTTAGTGAGGCTTTATATCTGCCTAC
ATCTTGTTTAAGTGAAACTGAATGTGTCATATCTGGTTAATTGTTATCTT
TGTTATAGTTTCAATTGAGTGTCAATGTGTCATATGTCTATTTCTTTAGT
GGGTTACTATCTTTATGATGATTTTGGGATAGCCTAGTGGTTCCCTCTTC
TCCCCGTGATATAATATTTATATATATTTATTAGGGATGCCCTTAAAAAT
AAAACAAGGGGAAAACCAATATATAAGCACCTAGCCGTTTATTTGTGTTG
TGACTTTCTGTTCCAAAGAGCCTCAAAGAAGGCTATTCTGAGTTTGGAAA
CTTCCGGCTGTCTGCATATCCATCTGCTTTTAAGATTGTAGATTTTCCGG
ATCTGTGTCTTATAATGGTTACCTTCTTGATTTGGTGTCAGCACTATCCC
GATATTGTACAGAACTCATTCCTTGCTTTTATTATTGGTTGTTAAACTGT
GTTTTTTACAGACTTATTTTGTTATCTTAGCATCTTTAATTTATAAATCT
TCAAATATCCTTTTGTTTTAAGGACAGGAGCTATTATTAATTGTGTCTTA
AAATGGACACGGCAGTGTACTTTCAGCTTCTTAGCTTTTTGTACATGTCA
AATCTTTGTGGAATACTCATCATGAACTCGTAAGTGGTGAGAACGTCTAG
TTTTATAGCCATTTATTTCTCTACAAAAATGATTGTTGCACTCACCCAAA
ATCTTTTCATCCCAATCAGTAGTGGGTCGCTTTTCTAATGCAGTGCAAAA
CTGTTATGTGTTCTTAGTAATGTCGTGATTCATGAAAATTTTATTTGTCA
AGACAAACCAATTTGCTTTTTTTTTTTTCTTCTTTGAAGCAGATTTTGCT
ACCCCGACATTCATGTCCTTAATTTGTTAGTTTAGCCAGAGATGATATTG
GATGAAAAGTGATGATCAAATCTGCTCTAATTTATTTTTTGTATCTTGTT
TTTATTTTGCATATATTTTGATTGTGTGTGAGAGCGTGCGGGAAAGTGTG
TTAATGGTGTCTGCTATTCGTTTAATTTAATCTTAGTTGTTTATACATGC
AAGTCACTTATAAACTCATTCCCAGATATGTTTGTCAAGCTAGCTGTTGC
GGTAGTTGGCGGTCTTCTAGGTTGCATATATGTGGTATCAAAGAGACCTC
CTTCAAAAGTTTGTGGATCACCAGGTGGTCCCCCTATAACTTCACCCAGA
GTAAGGCTCGCTGATGGAAGGCATTTGGCTTATAAAGAAGTGGGCGTTCC
CAAGGAAACTGCCAAGTTTAAAGTCATAATTATTCATGGCTTTGCTAGTT
CCAAAGACATACATCTGCCTATTTCTCAGGTATCTCTAGTACCAAAGTCA
CGCGTGTAGAATTCAGATGGCATATTTGAACTTGTTTATATATTCATCAC
TGCCTTAGGTTTTTATATGTCATGGATATTGCAAGTTTTTACATTTTTCT
TGTCATTTAATTGTTTATCTTTTGGTGATATTGCATGTGTAATTGAGTGC
TCCCATGGGCTAGATAATAATGTATGGGGTGTGATAGTATTGAGTCTAAT
ATGTCCCCTTCAGTCCTTGAATCCTAGCGCCAGTGGGTTCTGCTTGCAGA
GGCCCGTCTGGAGTTTTGACAGAGTAAAAGAAATCTTCGTTTTCGGAGGT
GCATCATTAGAATTTATCTTTGTATCTGAGTTGCATATTGTTTGTGTTAC
TTAGGCTTACACCACCATATCAAGGATTTCAGGTTTAACAGGGGGCGCAG
TGTTAATTTTAACCATCTTTACAACTGCTTTATTAGATTATATTCATAAC
ATTCACCTTACACTTTGATGATCAGTTTATAAGATCTAAAACTCTTGGCT
ATGCTCTTAGCTCTCTATTTTAAGATTTTTAATATTAGATTGCACCATAT
TATTTTTGTCCTTTCGAGTCGGTGCATTTCCTATCAGCTTGTTCCAGTTT
AGTGCAAAGTTCATGAAAAATTCCTTTATTTCTTAGACTTGTCACAGAGA
AGGATATTCTTTAACCATCTTCTCAATGGACTCAGACCAATGTTCTCGTT
CCCGTCAATTCCTTTGAGTTTTGGTCTTGCGACTGTGCTAAGCGTGCGAA
ACGAAAGGCAAAAGAGCATCAGACTTAGTTTTTTCTTAGCCTTATCACAG
AGAATGGTATCTTTAACCATGCTCTCAATGGACTCAGACTAGTGTGTTAT
GAAACTCAGTAAATGCAATAAATATTTAATCAAACAAATCTCAAGAATTA
GTTTGTGCATCGGTTACAGATTTGAAGGGGAGGATTTGTGGAGATAATTA
TATTTCAGCTTTATTTAGGGATTGAGTAGAAGTTGGAGTTGTAAATAGGG
AGGTCATTATATGTTTGGAAATGAAGATTTTAGACTGAAGTGTGTGCGGA
GAGTGGGTGGTTTCCCAGCCGAGCCTGGAAGTGTTCGACTCCGCTCGGCT
CGATTACACCCCTAGTTATGAAACACAACAAATGCAATAAATATTTAATC
AAACAAACCTCAAGAATTAGTTTGTGCATCGGTTACAGATTTGAAAGGGA
GGATTTGTGGAGATTATTATATTTCAGCTTTTTTTAGGGATTGAGTAGAA
GTTGGAGTTATATATAGGGAGGTCATTTATATGTTTGGGGATGAATAATT
TAGACTGAAGTGTGTGCAGAGAGTGGGTGGTTTCCCAAGGCTGTGTTTTC
AAGAGTGTGAATAATCTGATTCTATTCAGATTGTCATGAACTCTTTTAAG
GTCATTCTAACTATAAAGAACTTCTATTTTATCAAGATATTCCAATTTCT
AACATTGGCATAACTCATAAGAGCATATCCGTTCTTGGGGCCATGGCAAG
TTTGAAACAAATTAAAACTTGAATCAACGTTTTACAGAAGAAATTATAAG
CAATTTTGTTGGATATTGATTTCTTCAAAGAAAGTATGGTTATACTTAAA
AAGATAGACAGCATTAATCATGAAACTACTGGACGATCTATAATTACGAA
TGTTTTTGAGAATTCATAGCAATGTTTACCAAAATATGGAGACGTGTTTG
CGAATCAGGAATCTTTACCACAACGTCTTGAATTGCCTGTGTTTGAAGAT
ACATATTTGTTGTGCTATTCTCCTATACCGATATAACACACTAGCTGCTT
GTGACGCTACAATAGCTGCTATATTAGCTAAACTAGCTGTAACAACCTTA
TATATTGTAATTAAAGTACAATATCTATTATTCCTATAGCTAGTCTGCCT
AAATCATAACTTCCTTAATTCTGATCTGTTAGACTCCTGAAAACATTCCT
ATAATAGATTATGGAATTGCAGTCACAGGTGTAGAATGTTTAGTATTCCA
TAATTTAGAGGAGAAGACAGGTGAAAGATAAAGACCCAAGAAATTCAGGA
AGAGCCTTGGTTATTTGTTTCAGTTGTGTGTTTTTTTTTGTGTAACTTTC
CTGTAGGGCCCATATAGATTTAATACAATTTAAAATAAGTATTGTTAGTG
ATTATACGAGTGGTGGATGTTGATATTGTTAAACTTGTCCATCTTATACA
CATTCTCTGCAGTAATGGACCAGTGGTTTGATTCTTTGTATAGGCCTATA
ATGTCTGGTTCTTACCATTGTATTTAATGTAGGATCTTTATTTCAACTTT
CAGGAACTAATAGAAGAGCTCCAGATATATATCTTGTCATTTGACAGAGC
AGGTTATGGAGAGAGCGATCCATATCCAAAGCGCTCAGTCAAGAGTGAGG
CATATGATATACAACAATTGGCAGACAATTTGCAGATCGGTCCTAAATTT
TATGTGATTGGGATCTCGATGGGAGCTTACCCTGTCTGGAGTTGCCTGAA
ATACATACCACACAGGTTGAATCTTTTTTTCTAGCTTAGCCCCATGTTTA
GAATATTTTGTGTTTCTTTTTTCCATAAAATGCTTAGAATTCCTTTGAAA
ATTCGTATTTGCAGGTTGTCTGGAGCTTCACTAGTAGTCCCATTTGTCCA
CTACTGGTGGCCTTGTTTTCCTGCTAGCCTGTCCAAAGAAGCTTTGAGTT
TATTACTTGTGCAAGACCAGTGGGCATTTAGAGTTGCACATTATGCCCCT
TGGCTCTTCAATTGGTGGATGACTCAAAAATGGTTTCCTTCTTTATCTAT
CAACGAAGGTAACATGGCCATTTTCAGTGAACCGGATTTAGAGATACTAA
AGAATGCGCCAGAAACTCCAAGTACTGATCAGGTATATAGTTATTAACTT
ATTACATGGCATAGATGATTCTTTTGCACCAACTCTGTAGCCTGCAGGTT
AAGCGATTCTCTTTTTAGTTGCACCAACAAATGATTCTTTAAAAAATAAT
AATAATTACTGCATAAACTTTTGCACAATGATCAAGCAAAAAAGGGTTCT
TGTAGTGCGGCACAATGAACACCCCCCCCCCTCTCTATAATTGTGGCCCT
CCGCATCCTCTCTGAAACTACTTTGTTGTCCTTTTCTGTTAATACCCTAT
AATTACTAATTAGGAACACAAATTTTTTTGTCAAAGCTCAATCATGTACC
CTCTTCTTCAAGCCCTGACAGTTTCACAGGGAACCAAATTGTTGCATATT
GACTGCAGAAAAAGACACTTTTTCCTGTTTGAGCCAAAAAAAACTAGACG
TTTAATCAAACATCGATAAAAAGATAAAATTACTTGGAGCATGGAGAATT
ATACACAGAATTCTAATTCTGGTAGGTTATTTGGCTAGCTATTGAGTGAC
CGAGGAGGAAGAGTAGAGGGCTATTCAGTGTTGCTACTGAAAGAGGGTAT
GGACATAAACTTGTTATTTTGTTTAGTAACTTAAAATGGCAATGTATGGC
AGAGATTGCAGATGGCAGCATAAGAGCTCTAACCACAAAGCTAGAACACC
CGAGTTAATCCATTCCACAAATAGATTCATTGATCAAAGCTGAGTGAATA
GTAGATATATTTGTGTTGCATGTCATCTTAAAACATATTTTTGATGAGTT
TTAGTAGAAATGCACAAGACGATAAATCCATGGAGACTTAGAAGTCAATT
TATTTATTTTTGTTTTACAAACATATTAGTTTTTTTACGAAGCATGCAAA
ACTTCGGAACTTCCATAAATAATAACAAATTTGAAAATTTTGCTTTTACT
TCTCTTAACAGATTCTTTGGTCATCACTTATTATTTTACAATGTGTTATC
CAGGAAAAGATAGTACAGCAAGGAGAGTACGAGTCTCTGTATAGAGACGT
AATGGTTGGATATGCGAACTGGGAGTTTGATCCAACAGATCTTCAAAATC
CTTTCCCCAACAATGAAGGCTCAGTTCACATTTGGCAAGGCTTGGAAGAT
AAGATAATTCCGTACAGCCTTAACCGTTATCTCTCACAAAAGCTTCCATG
GATTCGATACCATGAAGTTCCTGATGCTGGACACCTTTTAGCATTTAAAA
GAAACTTTTGTGAGGCTATTATTAGGGACCTATTACTTAATTGAAACTGT
CTCACATTGATAATCCTGATTAATTAAAAGGGATAATGTATAATAAACAT
CACATTCTAGTAAAATCCTGCTGCATCATTTCTTGTATACATATTGTTTT
AGTTAAAGCATTACTAAA