| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017389916.1, is a part of gene, LOC108217066. |
| The genetic_marker, MK004037 K1481, is located in gene, LOC108217066. |
| 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_017389916.1 | XM_017389916.1 | mRNA | DCARv2_Chr4:8607021..8613047 |
TTCTCTATTCATTTCAAAACCCATCTTCAATCTTTCCCTTCTCAACCCTG
TAAGTATCTTTATCTGTATATTATATATAGTACATATAGTATGTGCTTAT
GTGTGTGTGTCACTGTGTGTTTCTGTTTATTAACAATGTAAAGTTTGAAT
TATGATGGTTGCTAATGTGTTGTGAATTGAGATGAATAATGGGTCTATAT
GGTTTTCGAGAATTATGATGTCAAGTGTATTGCATTGGTGATCTGTCTTG
AATGTGAACAGATATATAGAAACATCACCGGAATTTGTTAAATTAATTTT
AAATGCTGGTTTGATGGAATGAACTTGTAATGGCGAAAATGGTATCCTTA
GGAAATTTGGCACGTATTGAAAAAGGCAGGACACGTGCGGCAAATGCATT
GATCATGACTCCCTCCTTCCTACTTATTTGGCCCTTTAGACACCAATTCA
CTTATGTTTTATTTAATCACATTAATCACATTATGTGCTTATAGTTTCTA
AAGCACGCAATAGAAAAATTTTCAACTAGTGCGAGCTTTAAATTTTTGTA
AATGTTTTTTAATAGTTCAACTGTTCGGGTGCGAATGTCATAAAAAAGTA
AGTGAGTTTGCTAATTTTGTGTTGTATAGTGGCTTAAATTGATGATGTAA
GAATTATTATATGATTGTAGATAGCAAAACGAAATAAAATTGTTAGAAAG
GTGATAATATGCTATTTAGGGTTATCTAAATTTGCATACAGTATCATTTC
GGGGAGATGATGGAAGAACTAAAAAAACACATAATTTAAGGTGCAATAAT
AGAGAACATCTCTGTTGTGGATACTCTTTTTCTTATTGTGATATTAGTTT
ATAACAATATATTTTCAATTCTTAAAGTTACAATTGATTAAGATTTTAGG
TGTACATCTAATTAATGTGTTCAAGTTTATTAAATGAATCAAAATATTCA
ATTTACCATAAGAGTGAATGTGGCGAAACATTTTGAAATAAGTGGAATGT
GAAAGGGGCCACAATAAGTGAGACTGAGAGAGTACAGCCTTTCTTTACAC
CAAGACACATAAAAATGTTATTTAGCCAAAGAAATGCATTTAAACTTCTG
GGCTGCTAAAGAGGCCAAGTTGTTCAGATTTACTATTTTGGGACTTGCAC
AGTTGCACGCTATTTTGGGAATTCTGCCATGAAATGAGCACATGAAACTG
GATTGAGTTATGTGGTTGGATAAGTTAGTACATTTGCTAGAGATTGTACC
CTTTAGGCTGTTTCAATCCTAATTTCAGTGTACTTATTATTATCGTTTGT
ATCATTTTGTTAAGCTTGACTGCTTGAGGACTTAACGTTTAAGGTTTAAG
TATGTATTTGTAATGCATTAGATTTGAAGAGAGGATATATATATAGGCCT
TAGCCACAATGAAGAGACTTTGAGGGAGAGCAATGAGATAGAAACTTGGG
TAAAAGATACACGGCCTGAGATCAGTTCATAAGTGTCATAATGTTAAGTT
TTAAGATAATATAAGAATATTTGCTGACAGTGATGTAGAAATTATTCTTT
ATTGAAGGGCACAGATAGTTGAAAAGATTGTTATTTACACATATACTAAG
TTATCTATAATGCATCACAAGAAGTTCAAATGTGGTATTGAGTTATAATT
TCGAAAGACTTGTCCAAATTATCTATTTAAGACTCGTGGAAACTAGATAG
TAAAATTTTGTAGGGGACTCTGCTTTAGTACGTGTCTTAGAATTGTTCGC
GCTCATATTCATAGAGGACTACCTAAACCCTTATCACATACATTTTAGTT
AAGATCTATGATGAAGTTTCTGTTTGTTCATCATATCCATGGTCTACAGA
TATCTTATTTTATGACTCTTTTAATTTCAGTAAAGTATAGGGAGACTATC
TACTCTCGAGTGCAATGCTCAGCAACAGTGACAACCGTGCTTGATACACC
ATCTTTAGAAGCTCATTCAAATTCAGTTGCTGCGAACAGATCATGGTCCG
AATCAACATCAAATGCAGTGCTCGATTTGGAAAAGCTACATTTAGCATCT
TTAGAAGTTCATTCTAATTCTGTTGCTACAGACAGACCATGGACACATAT
CAGTGACATGGACCCTCCATCTGAGGTCAGTAATCTTCTAGACTTAAAAT
CACAAAAACAATATATGTATAGATTTGAGCGGGCCAAAAAAGAAAAGGGT
CACAGGGTCCCTGGGTCCTTTGCCTCAACTTTGTCATGAAATTTGTGCTT
TCTTTTATTGTATTAGGAGTTCGTACAATCTATGTACTGGATAAAGTCTC
TATTACGTTATAATATAGATATTACTTCTAATAAATGGAATAGTTAGGCT
TTTATATAAATTTGGTCACCACAACTATCAGCTCATCCCGGCAGGCAAAA
GGTTGTTGCAGATGTATAACTTTATGGGTATTGTAAAGAATATGTTGCTA
TATATTTCTTTTTCTTTCTACATCTAAGTTGTGATTTATTGGACGTCATA
CTTATTTTTTATCACTTTATAGTTTACATTTTGGTCAACAGAATGTAAGT
AGTCTTTAAGTAAGAAGGTTCTGTTACATTTATAGTCCTTAAAACATAAA
GTCTTACTTGCTCAGTGGAATATGTTTTTTACATTGTTGAAGACGAATTC
TACCAAAATAATTATTTTATTCAGTAATTGATTCAATATACATGTGTAGT
TGTTTGTGAGCACCAAGTTCTAAAATTATGTACAATAAGAAGTTTGGTAA
CATTTGAAGTAAGCTTTGTCCTTTGCCGTCTACAGATGTAATTTTTTCCT
ACATTCAGCACTCCTTCCAATTTTATCTCCTTCTGGCAAAAATGATATTT
TTGTCTAGAGCATGTCTAATGGTCAGACCAGAGCAATATCATGATTAACC
TTAGGCCCTAGTTTTGTGTTTGTACCATATTGGTTGTCGCGCTAATCGTG
GAATGCGCAGTCACACCACTTTCCTTTCATCTCAGAACAGGATAGGCATT
TTTTGAGGTCTTTATGCATATTCTGATTGGTTCAGATGCGTTATTGGAGA
AGGAATTTTCTTGAACCTGAACTTGTGAATGGGCTTGCCATATAGTATGC
AAGCTGCCTTTATATATAAGATCACTCCACAGCTGAAGCATTTAAGATGT
ATAACTAATTAACTATAAGTTCGTACTCGATCGAACACTTGAGCAAAAAA
CAGAAAATGTGGTCATTTGGTTAGATTACTTCACTCTCCAAATTAGATCT
CGAAGTCCTTACAGGAGCTGCTATTTTTGAACAGGCAACTTTGCCTATGG
AAAATCTTCTTACAAGTGAAGAGGCTGTCATAGCTGCTGCAGCTTCGGAA
GCAGTGGCTCTAGCGAGGGCAGCTGCAAAATCTGCAAAGGATGCTGCGAT
GATAAATAGCCATAAGAACTCAACAAAGATAGATGTAAAACCTACAGCAC
TCACATATGAAGCTGTAGATTCTTTATCCGAGAGGCCTGAGCTGACTCAA
TTGGGTGTAGCAGGAGTGTCCCAAATATCTCAATCTGAGGGCAGATCTGA
TGTTGAGGAGCCAACAGTTGAAGAACTTCAAATTCTGCAGGAAGAACTTG
GAAAAAGTATTGCTGTAAGATCGAGTCGTCAACCAGAACGAAAAGCCAGA
CGAGCAAGAGCAGCTGAGAAGGCTTCGGCCACTGTAGTTTCTGTTAAATC
TGGTTCCATGAGCAAGAAAAAGCGTGCTTCCCAAGAAATAGACCACTCTG
ACCCACTGCGGTACTTGAGGCAAACCACAAGTTCTTCTAAACTTCTTACT
GCAACTGAAGAACAAGAGTTGTCAGAAGGGATACAGGTTCTTTAACATCT
ATATACTCACCAATGTATATTTTTGGAATATTATTCTCATTATCACAATG
CGTCTACCAACTGACCAACATTACATTGTGGAGGTGAATGACACGCCTGT
TCTTAATGCAACTATGTATCATATTTCAAACACGTAGTTTATTGAACTTT
TATTAATTTTACTAAATATCTTCTTATATGTATCATCTTTAATTAAATTA
TAGATTGCTTGAGACAGAATATAATAGTAAGCTACTTCTCGGAAATCTTA
GTTATGATATATGATATTCTAGATTTTAGCCCTTTGCCAAGTCGATAATT
TGACTTTGTAATATGAAACTATTATTTTCTGAAACTATATATTCCCAATT
TGTATAAAAGATAAATGTATTACAATAAAAATATATTATATGTATTTTCC
TGATACAAGAAGTACTTGAGCAAATTACTAACTCTTATGGAAGTGCAATT
TTGTAGATAGAGGAAATATCTCATATTTTTAATATTAGCTTATCTATGGT
GAAGATCTTGATTACTCTCTTCTGAAAGCAATTTTTTATTTGTGAAATTC
AGGCTCTGTTAAGACTGGAAAAAATTTATAAGGAGCTTAGTGAACGTTAT
GGGGGTGAGCCTAGTTTCATTCAGTGGGCTTCCGCAGCTGGTGTTGATCA
AATTACTTTGAGGAGACAAATAAATTATGGCAAGTTCTGCAAAGACAAAA
TGATTAAGAGCAATGTGCGGCTTGTTATTTCAATTGCCAAAAATTATCTT
AAATCAGGCATGAATTTACAAGATCTTGTTCAGGTGCCAACCCAATATAC
AATTATACAGTTATAAGTTTTGTATTTCATTTGATGGATTATTGTACCTC
TTACGCTTTTCATCCAACGAAATGACACTGAACTGATTTTAATACTGTGG
TGGTTTATACCTTCAATTCTCAGGAAGGGTGTCGAGGGCTTGTAAGAGGA
GCTGAGAAGTTTGATGCTTCGAAAGGGTTCAAATTTTCAACCTATGCTCA
TTGGTGGATAAAACAAGCAGTTCGAAAGTTTCTCTCTGATCAGTCAAGAA
CTATTCGTTTACCTGTAAGCCTATCATCCAGAAATTATATATGCTCAAAT
ATTTTAATACATGTAGTGCATATGTATCTTTTTGCCAATTATGTGTGAAT
GTGTGTGCTTTGTGCTCTGAAAGGTTTAGATGCCCTTTTTCAGAAATGTC
ACAAAGAAGACTAGTTTTCAGAAAATGTGTGTTCCTGTATTGTAGTTAAC
TATGGAAAGTTGAGTAACATTTTGGGAGCCACTGATTAAACTTGTCAAAT
TTCTGCTCTACTTTGCATGCTTCTAACTTACTAATTTCTTTTTCATGCAT
CAACAGATATACATGGTAGAGGCGGGCTACAGGGTCAAGGAAGCAAGACA
AAATCTGTACAATAAAAATGGAAGGCAAGCTAGTCATGAAGAACTTGCAG
AGGCAACAGGGCTCACCATGAGCAGACTGTCTAATGTCTTACTAGCACCT
AAACCTCCACGATCTCTTGACCAGAAGATCGGGTTTGACCTTGATCTTAA
ACCTTCGGTGGGTCCCATATTCTTTAACGCTAACAACAACATTCTTTTCT
CAACCTCTAAGGCTAACTCTTTTGCTATCTCCTTCCATAGGATGTGATCG
CAGACCCTGAAGCAGAAACTTCAGAAGAATTACTTATCAAAGAATTAATG
AGACAGGACCTGAACAAGGTGTTGGATACATTAAAGCCCCGTGAGAAACA
GGTGGTCAGATGGCGGTTTGGACTAGACGATGGGAGGATGAAGACACTGC
AAGAGATTGGGGAGATCATGGGTGTAAGCAGAGAAAGAATACGGCAAATT
GAATTATGCGCATTTAGAAAGTTGAAGAACAAGAGGAGAACGAAAAGTTT
GCAGCAATACATAATTGGGTAACTTCCTACTGTAAATCAGAAAAATATAT
GAGCAGATAGACCCAGCCACAACCAATTCTTGAGGGACAGTGGATGTAAT
ATGTTTCTTACTTTAACTATCTGTAGTACATCTTCCTTTTGGCCATAACT
GTAGAATTTAATCTTGTATAGAAACAAAGAAGTTTTGGATAAGAGCATCT
CCAAATCATTCTGTGTAAGCTGCTAGAAAAAGATGAGATATCTTTTTGAG
TTGTTATATATTTTATATCTTAGACA
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