| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017393208.1, is a part of gene, LOC108219707. |
| The genetic_marker, MK002154 ESSR-049, is located in gene, LOC108219707. |
| 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_017393208.1 | XM_017393208.1 | mRNA | DCARv2_Chr5:4049889..4055765 |
AGTACATAAAACCATCTTATATTCTTCTTACACGCAGTCGCGCAATTAGA
CATCTCACAACCCTAAAATAACATCAAAAAATGGGTCGCGGCCGGAAACG
TAAAAACGACACCGTCGAGCCCCAAGACACCCCCAACCCCCAGAACGACG
TCGTTTTCTCCCTCAACAAAATCGAACTCATCCACCCCTCTACCACCACT
TCCGCCGCCGCCGCCACCACCACCACCACCAACCACCCAGCTCGCCGGCG
AGGCCGACCCCGCAAAACCCAACCCCATGAACCCAATCAAATAAATTCCC
CAAAACGACAAGCAATTGATCAAAACGGCAATGCCAACGGGGTTGTTGAT
CATCATGGTTCAGAAGATTGGGAGAATGTGGCTAAAGTTGTGCCCGAAAT
GGAAGCTGTGGTGAAGGTGTTTTGTGTGCATACTGACCCGAATTTCTCGC
TACCGTGGCAGCGAAAGAGGCAGTATAGTTCTAGTAGCAGTGGCTTTGTT
ATTGGGGGGAGGAGAGTTCTCACAAATGCGCATTCGGTTGAGCATCACAC
GCAGGTTAAGTTGAAGAAGCGCGGCTCGGATACTAAGTATGTGGCCACTG
TGCTTGCAATTGGGACTGAATGCGATATTGGTGAGAATGACGCTAATTTT
GTCAGCATTTTGTTTCGTTTCATCAGCTAGGTGGATAAATAGTGTTAATT
GTTGTATTAGAATGATTATATTATGAATAATGTGTTATATATTGTTGATC
ATGTTGGTTACGTTAACTAGGTGGAGAAATAGGTATAACTGTTGTATTGA
AATTTTCGTTTTGTTGTTATTTGCTTAATCATACTATGACTGTATTGTAC
ACTTCTAATCAAGTTCGTTTCTATATAGTTTTAACTGTTGTGTACTTGTA
TTAGAATTTATGATTCATTGATATATGGTTGATTAAATTATGACTGTGTT
ATATATTGTTAATTCTGCAATTATCTATTCGTTAATAGGTTACTAGACTT
GGTGCTTGTTTTTAGGATTGGTATATTTTGTCAGGCAATTTTTATTGTGG
TATTAAGTCTAAGAATTTATTGACAGCTGCATAAATGAATAGAATTTGTT
TTTTTGACTGGAATTGGTGTGTATAAAGGTTTTATAGGGGCCATGATATA
TGCATGTGCGTGCAGTACTGGGTGAATAAGTGTTTAAGATGAATGTGATT
TTGTTCGTTGATGTTTTTGTTTGTATATTTATTTTTTATGAGTTTCTAAT
TTGTGTTGCAGCTCTGCTTACTGTTGCTGATGATGAGTTCTGGGAAGGAG
TTTCACCTGTTGAATTTGGCGATTTGCCTACACTTCAAGATGCAGTGACA
GTTGTGGGTTACCCAATTGGTGGAGATACTATTTCTGTCACAAGTGGGGT
GGTTTCACGAATAGAGATTTTATCATACGCGCATGTATCCACTGAGCTTC
TGGGATTGCAGGTGAGTTTTTTTTTTTTTTTTTGCACTTTTACTGCTAAA
TCATATTGTCTTGCATTTCAGTTATGAAGTTCTCACAACTTAAATTATTT
ACAGATAGATGCAGCTATCAACTCTGGGAATTCTGGAGGACCTGCCTTTA
ATGACAGGGGTGCATGTGTGGGTATTGCTTTCCAATCCCTTAAACATGAG
GATGCTGAGAATATAGGTTATGTCATTCCAACACCAGTCATTAGGCACTT
CATCCAAGATTATGAAAAAAATGGAGGATATACAGGTATGTTATGGAAAA
TCACTAAGGGTGGCTTACAAGTTAACCCAACTGTTTAGGGCTGTCAAACG
GATATTTAGGATACGGATACAGCTATATCCGAATTCGAATCCGGAAGTTC
GAAACCGTATCCGTATCTGGAAATATCCGGCTAATATTTATTTGTATCCG
AATCCGTAAGATATTATCCATATACGGATAATATCCGGATCCGAAATCAT
TTATCAAATATATTTTTTATAAAAGTTGTCAAACGGATTTCAACTGAACT
TGATGTGCATTGGAGTCCAACTTGAAGCATCAGCTGCAATTTATTAAAAG
TGTGTAAGATGATGAAATGAAAAGATAATTGAGAATTCAAACAGGAGATA
CAAACCTCTATCTTGTTCCATTGACACTTGACAGAATTCCTAATCAGTAA
TCCTTTAAGAATTAAAATGTTGATATGCGGGGTTAAGTAATTAGGGCTGT
GGATGATACCAGAAATAGAATCAGAGAAGAGTGTGACTGTGGGATGTGGC
GTGAAAGAAAAATGAAGAGGCGGCCAGGCGGGGATGAGGGATTTAGGGAT
TAGGGTGAACTAGTGAACTGGTGAGTGAGTGCGTGTGTCAAAATGTTAAT
TGATTTTCAAATATGAATATATGATGTAAACTGCTGAAGTATATATGATA
CTCGTATGTATGGTAAACACTTAAATAAATACTATATTTTAATATTTTTA
ATAAATATATAATAAATATATTAATTAATTAATTAATTAATTTCAGATTC
GGATATTTTCGGATGCGGATGTGCCTATATCCGCATCCGTATCCTAAACA
TTCGAATTTAGATACGGATAATATCCGGTTTACTTCGGATACGGATAATA
TCCGCTTTTTTTCGAATACGAATACAGATATTTCGGACGGATATCGGATT
TTTTGGATTTTTTTGACAGCATTACAACTGTTCATGTGTTACTATGTTAG
CTAGGAATATTTATAAATCATTATTATGATAACTTAGTCAGAAGCACATC
CCTACTCTATTATAGTGCATTCAATAATGTCAAGCATCTTTAATTCTTTA
ATATTGTGAAAATTACTGACACTGCAATCTACTGTTATCTTGCACTGTAA
TTTGAGCTTGTGTAATCTGTAGGTTGTGTGAGCAGCACTGTTTTAGTTGC
AACAGTTGTTCAGATATATTTTAGGAGTTTATGCTTGTTTTTGAAATCGT
TTTGTATATTTATTATTTTGTCATATTTTACCTCCTGTGTTTTACTTTTG
TGATACAATATCTGTTCTACCAGGGTTCCCTATTCTTGGGATTGAATGGC
AGAAGATGGAAAATCCAGATCTGCGCATGTCAGTGGGGATGAAATCTAGT
CAAAAGGGTGTTCGAATACGAAGAATTGATCCAACTGCACCAGAATTTCA
GGTTTTAAAGCCATCAGATATCATATTAAGTTTCGACGGGGTTGATATTG
CTAATGACGGGACAGGTAGGATTTTTTTTTTGTTCCTTATTATATTTATT
ATATATGTATTGTAGTGCTAGTGCTAATGTTTGTGTCAATAGCTTCTAGG
CAGTCCTAGTATCCAGTTTCTCTTATTATATGTTTTGCTTGGATAACTTT
TTAAGTTGGTTTCTTTGGGAATTTGTGAAGTGTCTGCCCTTTGCTAATGA
GATTCCACTTTATTCTGTGAACTGTGAAGCATTTTTTTTTTGATTAGCAA
GTTTGGTGTTTCTCTAGGATTTTATATATTTCTTACTGATTTTGCTTCTT
GTAATTTTCAGTTCCATTTAGGCATGGAGAGAGAATAGGTTTTAGTTATC
TTGTTTCACAGAAATATACGGGAGAAAGTGCAGCAGTCAAAGTTCTTCGC
AACAGTGAAACACATAAATTTGACATCAAACTCGAGTCGCACAGAAAGCT
TATCCCAGCTCACAACAAAGGCAGACCCCCTTCATATTACATTATTGCTG
GATTTGTTTTTACAACCGTATCAGTTCCATATCTTCGTTCTGAGGTGCAC
TACCATATCAAACTTTGTAAACAAATATAAATATATATATATATATATAT
ATATATCACACTCTGTATACATATATATATATATATATATATATATATAT
ATATATATATATATATATATATCTACATATATGTATATATATTATCCTGT
GATTAGAATGGCGTAAATACCAACTAAATTAAGTTCATCACTTGCATATT
ATCTTTTGAGCATTCTGTTTCTTCCCTTGTAATACTAATGAAAATTTTAG
AGGCACCAAGAAAGTAGTGATTAAGATGTTCGTCTTTTTAGTAGTATATG
GAAAGTGAATGAAACGAGAGTAAGGCTTTTTACCTACAACTTGTGGTGCT
TTATGTGCTAATACCAGAATCAGTGGTTATATGTATATTTTCTTCGCAGT
TTTAATTAAAAATACATTAAAATTAGATTAAAGAGGTGATGATCTTGTTG
CTTATTAGTAATAAACTGTAGAAGTTTCTAGATGATGGCAGTGAAACAGG
GAGGAATAGACAGTCTGAATTATTTTAGAAAATACCTTGTATGAAGTATA
TACATGATATTAAAATGAATTAGATGCAATGATCTGAATATAGCATCGAG
TGACGGCGGCGAATTTCCGAACTTCTGATTTTGAAGTAGAAGTTCCCTTT
AATGAATAAGGCAATATTCTCGTTTGGCGCACAATTCCTCCTTGATGTTC
CTTCCTAGAAAACAACGAGATAACTATATCTTCTAGACAGTAGTTTGTTG
ACTTTCAGCTCTCAATAAAAATAATTTAGGGAGTATGAGTTTTGAAATTT
CTATAATGGACGCTAATGAGTAGGTGACTTGCCAATTTTGCTGGAGCTCT
TCGGCCTCTGTTGCTGTTTAAAGAAAAGTTAATCGACACTTGCATAATTA
TTTAAGTATCTTTTTAGTTGTTACGAATCAAAGTATGTAATGGTTGTTAC
TTATCCTCTATTACCTAATGAAGAACCTCTTTTTGCGTGCTTACTCAGTA
TGGAAAAGACTATGATCTTGAAGCTCCAGTCAAGCTGTTGGACAAACTTT
TACACGAAATGCCTCAATTTCCTGATGAACAAATTGTTGTGATTTCTCAG
GTTCTCATTGTTTTTTTTATACATACCTATGATGTTGTTGGGCGTAAGTT
TAATTGGAATTGTTATATCCTATGTTACATGTGTTCTCATCTCGTCAAAT
TATTTTTAAAGGTACTCGTTGCAGATATTAACATAGGATACGAGGACATT
GTCAACACCCAGGTTAGTTTTAATTGACCATGCGAATGTAGTAGCCTGCA
TTAAATCGCCTTGTCTATTTGACGCCCACCCTCTGGTTTTGCTTAACACA
TATATTTAGGTCCTTGCTTTCAACGGTCAGCCTGTGAAGAATCTAAAGAG
CCTGGCCAGCATGGTAGAGAATTGTAACGATGAGTTTTTGAAATTTGATT
TGGAATACCAGCAGGCATGCTCTCTTTTCTTGCTTCCCCCTTTTAAAAAT
GTCTATTTTTAAAAATTGTTTTCTAATGTATATTAATTATGCAGATTGTG
GTCCTTCAGACAAAGTCAGCGAAAGCTGCAACGTTAGACATCCTAACGAC
ACATTGTATACCATCAGCCATGTCTGACGATCTCAAGTGATCAGGTTCAT
ATGATGGTGATATTGACATGGGGTCTTTTGAAATGTTCATTCCTTCTCGA
ACCCCTTAGTTCCCAATTCACACCAGATCTAGTTCTATGTGGAGACCGAT
TTCTCATATAGATCTAGTTCTATGTCAAGACCGAGTCAACCAAAAAGTAT
CTTCTCTTGTGGTTGCTATATAGAATGCAATTTTGTGTAGTTCGACTATA
TCATTCTGTTAACTTGTGGTTGATAAAAGTTTATAGTTATTGATTGTGAG
CTTTGGGTAAATAATGTGACAGTGACACCAGTTTTGAAATCAGTATCTGC
TTGGCAGCCTTGTGCTCGTTTCTTTCGACTTATATATTGAACACTCAATT
TGGAGTGTTCTGATGAGAACTTTCAACAAGTCTTGCATAGCAAGTGAACC
GAAATTCTGCAAAGTTTCTAGTGAAACTGTGGTCGGTCACACATTGGCAC
CAATTGAATCATTCCAAGTGGAAAAA