| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017359278.1, is a part of gene, LOC108192791. |
| The genetic_marker, MK004083 K1527, is located in gene, LOC108192791. |
| 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_017359278.1 | XM_017359278.1 | mRNA | DCARv2_Chr6:3409400..3415946 |
ATATATATTATTGTGTTAAATCACGGGTACAAGGGAGAGTGCAAAGTAAC
CTCGCCTCTTATAATTTGAACGAAGAGTAAAGGACAGTGCAGCTGGTCGT
CCTATCGATCCCCCCCACCACATCTACTATTAGCGTCGTTTTTCTTCTCC
AAATTCATTCTCTGCCGGTATGTTTTCTTTTCATCCCATCTAATCTCAAC
CTATCTTATCCTATTTACTTTTTTTAAAACTAATTTGGACTTGATCTAGG
GTTTACGTTAATAATCCCTCTCTCTCTCTGATTTAATTAATTAGTTTTTT
TAGCTCAAATAGATTAAAAAGGAGACCCTTTATTCTAATTTGATTGTTAT
CACGTTAAACATAGTTAATTGAATTCAATTTTTGGATTTTGTGAATTTGT
AATTCTTGAATTGTTGGGTTTTGTTTAGGAATCTCATATTAGACTGGTTA
TATATCTACATGGTTTTGACAACATGGGTTGGCAATATATTTTTAATTGA
GTTATTGTTAATGTTATTCTTGGTTATCTCGGTCTCAGAGGTTTCTTTGT
TCGGTTATAATGGATGATATAGCAATGAAATAAAAATAGTCAAGGCGGGG
GAGAAGGATGTAAGGAGTGGATTTTTTTTTCAAAAGGTGGAATTTTTTTA
TTGATGAGTTTTGTTAGAGAAACGAGGACGGAAGAGGATGAGCATTTATC
CCTGTATTAGATGGGTTGAATGTCTAGCTTAACTGGTATAAAATGTGATG
CGGAGATAATGAAGATCATAAGTATAATTCACTGATCCATTCTTACCCAA
TTATATCCCCTAACTAAACGTAGGGTTCGAGATTAATTGATATACGGAAA
TATGTAATATTACAGTTCAAGTTGGAATGTTTACATTTACGTTGTACTTG
CTTGTAATGTATTTGCTTTCATAGATCTCAAATATGGTTGAAGAAGGAAG
AGTGCACCCAGATTGCAGAAATGCAGACAACCCATACCACATATGTAGTG
AATACTGTTTCACAGTTATTGCTGAAGCCAAGAAACATACTAGTAAAGCT
GATCTTGGTGAGTTTGCTGCTCTTCTTTTAGTGATCTTGTTGAATTAAGT
TTGTTATGTATTTCTCAGTATGGTACCATTTTCAAGTCAAATCCTTTTAC
TGCAGCAATGTCTTCTTTTGCCTTTCAACGTCTTACTCTGTCGTGTTAGT
TGTTGGGGAAGAATGTTTGCTCAAGAAATAACTAATTAGTTCTTTAGGAT
TCATATGTTGAGCCAATGTTTTGATTAAACAAATTGAAGGCATACCTTAC
TAGTGGTATACCTCACTAGTGTTTATAGAGCATATGGCAATTTTAATCGA
ATCTTGCAGTGAAAGGAATCCAGTTTTTAGAAGCTTCTTCTGTGTGGTCA
TGGATAAAATCAAGATCTGTCCACTTTTTTGGGCAATTAATATTATTTCT
TACTTATGTATGCATCTCTTAGGTGACCATCACCGTTGCTTGATATTGCT
AAGTGCAACATTGATATTATTTCTTACTTATGTGTGCATCTCTTAGGTGA
CCATCCGTTGCTTGATATTGGTAAGTACAACATTGATTGCAATTACTATC
TCGTTGTGACTGATAGCACTCCATTGTTATTACCTAATTAATTTTTTAAT
TTGATAATTTGTTGCTTCTGTCACAATTTTAAGGTTTATCTCGTCATGTC
CTTGTCTTTTTATCTCTGGTTTTGCATGTCTGGATCTATTTATCTTTCCT
TTATGTTTACTTCCAGTTGTTTTCATAATTTTCCTCCCAGATATGTTTTA
GTGATTATTTTTTGTCATTTTGAAATTTTGGAAGCTGATGTATGAGCACA
ATAATTGTGTTGTCTATTTTGGTATCGTTAGTCACTGAGATCTGTTTCTA
ATATAGCACCAGATTATCTAGTTTTGTTGTAGCATGATTATTCATTATTT
TATTTTATTTTATTTTCTTTAATTTGATGGCAATAGACAAGGCTTTAGTT
TTGTGCTTGGATGTATAATATAACAATTTATAGACCCTTTTTTATGACTC
AGTTTTCACCCCAATATACATGGCTTACCTTTCTATTATTTTCTATAGCA
ATGCAACCTAAAGATGGAAATCAGTCGGCTTCTGCTGCCAATCCAAATCA
GGGTGAGGATCTATTGGATGAAAGGCAGGCTAGTGAAGAAAAGACAGATG
CTAGTGATAGTCAAGATGTTGAACACAATGTGGATGTAGACTTTACCCAG
CTTAAAGGCACAAAGAGAAAGTATTTCGAACTAAAACTGAAAATGGTAAT
GTGGATTTGTTCTTTTTCTAATTTATCATTTAGAGGTTGCTAAATTTCTC
GTCATTTTTCTTTCCATATATTTTCTGATCTTGTATGAGTTACCTATATG
TAGAATCAAGCAAGAAAAGCCAATCAAACTGACATGATGGCTGAGAAGAA
AAGAATGGAAGCTCCCCAAGAATCTAGAGGCATTTCGAAACAAAAATGGA
ATGAAGAGAGGAAGAAAAAAATTGGCAAACTTCTTGATGCCAATGGTTTA
GATATGAGTAAAGCTTATATGCTGGATACTGAACAGATGGCAGAGATGAA
GTATAAGAAATGGGAAAAGGAGCATGCTCCTTCTGGTTGGGATGGTATGC
CTTTATCCCTCTTCTAAACAGTGTTACCTCATGGAAAAGTTGAACTTGTT
TAAGAGCTTTTTGGGTTATGTTAGTTTCCCAATGACTAAACACTTAGTAT
GACCTTTGGCAAAGAGGTCGTGGTCACTATTTCTGCATATAATATATTTT
AATCATTTTTTCAATATGCATCAAGGTACGATATAAAACAATCAAACACT
ATAAATCATGTTATAAATTCAAGTTGCAAGTTGCTGCCTGTAGTTTTCCC
GAAGTACAATCTGACTATCTTCTATCTTGCTGGCCACTATTAATTATAAA
GATTGGTATCATAATAATCTTTTCCACAACTTGTTAAGCATCTTAATTGC
ATTAGGAAAGGCTTGCTAGCAACTAGCAAGTCTTGTTAACGTTTTTATCA
CCTTGTAGATGCTATTATTGCTGGACCTGATGTTTAATGTCTTGCTTGGC
CAGTTTTTAACCAGAAAACATTGTTTAATGCGTACAAGAAGAGGACAAAG
AATATAGATGTTGATCTCGTAGAGTACAATAAAATGAAAGAAGCTGATCC
TGAATTCTATCGAGATGCTTCGAGTCTACAATACGGAAAGGTAAGCAACT
CTGCTTCTATGTTAGTCTTGTATAGGTTTTTATGACAAATGAAATGGCTA
TTTAGTCACTAAATTCACCCCCAACTTGCAGTCTCACTATGAGACTGAAA
GAGTTTGTTGTCAACATAATGAACCAATATTAAACTTATAGTTAGGTTTC
GCCATTTAAAGTGTTTACAAATGGATGTAGAACTGACTGCACCTGCTTAT
GTTTAAATGAAATTCCTGACTCTGTGAATCTAACACCCAACTTTCTACTT
GTATCAGGGTCACTAAATTTGCTTCTATCTAACTGAAAGTTGATTAAAAT
TTGTTAAGTTCTTAAGGATTATTTCGCTGCCCACTCATTTCTTTACGGTA
TTTTTCACTGTCAGGCACGCATTTAAGGTGAATATAAAGTAGTTTCATAG
CTTATTTTTTAAATTTTCTATTTTTGAATAATAATTTGAACACAAGATTT
CTACTCGGGAGGAAAAAAATTAAAATAATTTATGAAACTATGATTTATAG
GAGCATGCCAAACCCTCTGTACCCCAAATGTAAACAACTTGGGAGCGATG
AGTGGCAGAGGGAGCATTTTTTATTTTTTTACTTACATATACATATCGTT
ATATATACACTGTATATATATAAGTTTCTCAACTAAGAGACCAAGCTGGG
TTGTATTCTTCTTTTCTATTACGTATTTGATTTTAAATTGGCCTTGGACT
TTTCTTTTGGATTTGGCCGAAAATTATTATTTAATACTTAAATTTTTATC
AATAAATTAGTATGGACATATAAAATTGTACCGGAGTATCATCATAAAAT
AATGGGTTTTTCAAGATTAGATGTTAGATGTTTTAATATAAATGAAGTAT
TTTTAAGGCAGAATAATTTAATCTCTTGATTCAAAATAACAACAACAACA
ACAATAATAATAATTAAATGCAGGCTGGGTTTTTTATAAAATAACTTGTA
ATATAGTACTCTCGCTGTCCTTCTCATTTTTTACGGTTTGTTGCATTGCT
TGACACCCCTTTGAAGGTGCATATAAAATGTAGTTTCATAATTTTATTTT
TAAAATTTTCCTTTTTCTTATGAATATTTATATATTAAATATTTATACAG
AAGACCCTTACTATTTTACTTAATCGCATTGGTTTGTATTAAGTTTGTAT
TTTTTAGTAGTTTGTATTAGAGTAGGACCCTATATACATGCTTATTAAGT
CGACAAGTCGAGGCTCGGCGCCCGGATGCCTTGGAATCGACTAGTCGACA
AGTCGCCCGACTAATATATATATATATATATATATATATATATATATATA
TATATAAACACATCATTCAATATTTCAAATAGGAAAGAGATAATAAGTTC
AAATACCAAAAGTCAAGTATCCCTAAGCAAATAAAAACATAATAGATGAG
TGAAATAAACTAATCAAGCATGAAGTCATTAAATCTTCATATCCCTCTCG
AGTATTCTCTGAGGATGGCCGCAATCTGAGTTAAGCAGCAATTGGAAATC
AAAGGGGCAACCTTCCTGATCATGCATAATAGATCAGAATTAAAAAAATG
ATAATTTTTTTCCATTAAATATGAAGAAAAAATAATTAAAAAATAATCAT
TAAACGTTTTTAATAAAACTGGACTTATGAAATAAATAAAATTGTATAAG
TAAAATAAAACTAGAATTTAATTTTTAAAAATAAAAGATGAAAAAAATAT
GAATAAAAATTAATTAATATTAAATAAAAAATAATTATTAAAACGTTTTT
TAATATAATACTAATACTAATTAATAAAACTGGATGAAAAATAAATATCT
TTTTCAGAAAAAAAGAAATAAAATATAAATATTAAAATGTTTTAAATAAA
AGTTTTTAAGTAAAAGCATAATTTAGAATTAATTTTGAAAAGTAAAAGAT
TAAATAAAATCAAAAATGGAATAAAAAAGGTACATGTACTACCGTTGTAC
TGCCCACAATATATACACACACGCGACTGTGTGTATATACATCTGGGAGA
CTAAAAATGAAAAAAAGAAGAAACGGACAGAAGAGGGAGAGGAGAAGACG
AGAAGAGAGAGAGAAGAGAGAGAGGAATGGAGAAGGAGAGAGAGAGGAAG
CTTACCGGAGTCGCGGCGCAGCAAACAACACGTAAGTATAGGTTAAAACT
GGGTCGGGTTAAATCTGATTGGACCGGGTCGGTACCGGGTCGGGTCGGGT
TTGACCCATGTCCGACTTTTCTTCTCAGTCGTTCAACGACTAATTCATTT
TACCGACTTTCCGACTAGTCGACGACTAGTCGTCGACTCAATAAGCATGC
CTATATATGTATATATGTGTGTGTATATGTATATGCATATAGGATATATT
ATGCTAAGGGTTCTAAGTGGAACATGACCCATGTATATATGTATATTAAT
TTTTGGTCTTTAGAATTGTGTTGAGTGTTCATTATTTTGGGTTCATTTTT
GAATGAAGTGGGTCAAAGTAGTGGTTCAATGAGTTGACTGCAAACTTCGA
TTGGATGATGAATCTGCAAGCTGGGCATGAGTTTAGTCAATAAATTTCCC
CTTGACCCTTTTTGAAATACACGTCATTTCTTACATGGCAGCTGAGGTGC
AAGATGAAGCTGCATGATATTAGTCAATGACATTTATCTACATTAAAATT
TCTGAATGTGTAACCACTGTTCAATATGTAAATGTAGGTTTAGTGATTAG
GATTTTTATTTTGATGATGAAATTGCAAGTTAGGTGTCAGTTTGATAATT
AAAAGCTGGGTGTCAGTAATAGCCATTTAACCCTTTTTTCTTTTTTTTCT
TTTTTTACATTTTTAAAGGCGGTCAAAACTTTAATCACATCTATTGGCAG
GCACCAAAGATCTCAGAGGATAAGATTGACAAGATGGTGAAGGAGCTCAA
GGACAGGGATGAGAAAAGAAATACATTTAGCAGGAGGAGGAAGTTCCACG
AAGAGAAGGACATTGACTCGATCAATGACCGGAATGAGCACTTTAATAAG
AAGATCGAGCGAGCCTTTGGCAGATACACACTAGAGATCAAGAACAATCT
TGAGAGAGGAACTGCTTTACCTGATTGAGAGGTGTTCTGCAATTATGATC
CACTAAATGCCTCTGTTAAGTGTGCTTTAAGCTGAATTCTACTTAAATGC
TTGTATGTTAAGCAATTGTTCAGTTTACTGCAATTCAGAAATTTTATCAT
GAAGCTGAAGTATTTTGATAATACTTAAATGTATTTTCCGACTCGATGTG
TAATTTTATGATGTTTAAGATTGAATCGATATGAGATAGCGTAAAA