| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017367129.1, is a part of gene, LOC108199349. |
| The genetic_marker, MK003437 K0881, is located in gene, LOC108199349. |
| The transcript, XR_001802394.1, is a part of gene, LOC108199349. |
| The mRNA, XM_017367130.1, is a part of gene, LOC108199349. |
| 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_017367129.1 | XM_017367129.1 | mRNA | DCARv2_Chr8:17602788..17609041 |
| XM_017367130.1 | XM_017367130.1 | mRNA | DCARv2_Chr8:17602788..17605633 |
CCGATCAGTTTAACAGTAACCAAAAGCACAAGTATTATTCTGGTAAGAAG
AAGATAGAAAATACTCTACACAGAGCGCCTCTATTTCTCTCCATACAAAT
TTATTACTCTTCTCTCCCTTCATCCCCATTTCTTCTTTCTTTTACTTTCT
CTCTCACACACTCCTCACACACAAACACAATCCGTGTATTCATCTCCTCC
CCCCATTCTTAATCCCCCATATCTTCATCATCTACTTCCTACCCAGATCC
CCAAATTCACTGATCTACAAAACCCAGATCTCAATTTTTTTAATCATGTC
CAGATCAGATCTCGCTCACAAAATCTTCCCAGAGCCTTGTAATATATTAA
GTGATGATATAGACCATTTTGATTCATTGCCTGACTCTATTTTGCTCCTC
ATTTTCAATCAGATCGCTGATGTTAAAGCTCTGGGTAGGTGTTGTCTCGT
TTCGAAAAGGTTTCATTTTCTGGTTCCTCAGGTTGATAATATTCTTGTTC
GTGTTGATTGTGTGATTTCTGATGATGATTCATCTGGGGGTTCTTCGTCT
TCGAGCTCTGTGTCGAAATCTCACACACCCTTTTCGTCGTTGTTTCGATT
CGTGTTTGGTGGGATTGTGAAGCCCTTGCAATCGCTTACACAGTTTTTGC
AGTTTAAGAGATCGGTTAATGGGACTGGGTTTGCTGCTTCTTCGTCGTCG
TTATCGGTTAATGGGGAGGATTATGATGAATTGGATCAAGGGGGTGTTAC
CCATCATTCACCTACTCAGGTTTTGAAGAATTTTAATGAAATTAAGATAT
TAAGGATTGAGCTTCCGAGCGGTGAGCTTGGAGTTGATGATGGGGTATTG
TTGAAATGGAGGGCTGATTTTGGGTCAACTCTTGATAATTGTGTGATTCT
TGGAGCGTCTTCGGTGATGCCTAGTAAGGGTTTGGATGGAAATGGTGTTA
ATTTAATTAATGAGGATGATAATGGAAGTATACCTGAATCGTTTTATACG
AATGGTGGATTGAAACTTAGAGTTGTTTGGACAATCAGTTCGTTGATTGC
TGCTTCTGCTAGGCATTATTTGCTTCAACCAATTATATCCGAGCATAAGA
CATTAGATAGTTTGGTGTTGACCGATGGTGATGGACAAGGGGTGTTGTGT
ATGAATAGGGAGCAGTTGGAGGAGTTGCGGGTGAAGCCTTTGTCGGCTTC
TAGTGCTTCTAAGAGGACCCTTGTGCCGGCTCTGAATATGAGGTTGTGGT
ATGCGCCACATTTGGAGTTGCCGGATGGGACTGTGTTGAAGGGGGCAACT
TTGGTTGCTATTAGACCAAGTGAACAATCAGTGGTGAAGAAAGAGGTGGC
TGATGGGTCTTGGGTGTCTTCTGCGTTTGAGGAGCCTTATGGAACAGCTG
CAAAGATGTTGATTAAAAGGAGGACTTATTGCCTTGAGATGAATTCTTTT
TGATAGCACTCTGATGTTTCAGTGAGGTAAATCTTTAGACATTATTCTTT
GATTGACCATATTGAGTTATCATTTTTTTTTTTGAACTTATAAATGAATT
TTAGGCTTATTATCTTATCCAATAGACATCAAGGTCAATTCTTGTTAACT
TTGGCTCTTAGGTATCTGCAGATTAATGTGGATCTTAGACCTCCGACACT
GTCTGTGAATTTGCCTTTGCCCTGTTTTTTCTGATGACCCATTCATGCTT
GGTACTAGTGTGTTAAAATTTCACTTTTTTGTTGTCTTTATTTTTTATAT
AATCTGATCAACGTATGTCTGTAAATGTACTTACCGTTGATGATGGTCAA
TCAGTATGCCAGACACACCTCTTAGATGGTGTGTGGTCAAGAATTACTTG
TAACCAAAAATGTAATGCACCGTGAAGGAATATTAATCTGGCAAGCAGCA
CTCGTAAGATTTGAACCTGATACTCTTTTGAGTGTCAAACTATACACCAG
TAAGAACGTGCAACCGATGCTAAAGATTGAGCAATTAGTTTTTTATTCTA
TTGACATCCTTAGATATGATAAGGTTGATGACCTAATTTTGCAAAGTCTA
GACTTTGTTTTCCATTCATGCAATTAATGTTTGCTAAGTTTTTAATGTGT
TTAATTAACTTGCATGATCTTAATACTCTTATGTAATGCATTGGACAGGG
AAAGTATATTCTTGAGATGATACGATACAGTACGTGTTTTTGGGCAGGCT
GGTAATATACACACTTTTGTTCTATATCTTGCTAAATATTTGAGGGGTGT
TCGTCAATGGCAAATGCTAGCTTTCTTATCCTATCTGGATGCAGCCAGCC
AAAAATGTACCAAATCCATCGCCTAAAAACATCACACTCGTCTTGGGGGG
GTTGGTACAATTCTGGATCTTTTGCAGCCCTTGATAGTGGCACAAGCTTC
CGTTTTGTGATGTTTTACTACTAATCCAGTAATCCATATATTCTTCAAGC
GTAGTAGAATTCTTTAATGGTGCCATTATACCAACTCCATCCTCGACGAA
GGCATTCCACTATTAACATACACAAGATATTAGCGAGGATGCAATATCAT
GAATGAATTTTTATTCTTGAACCTCATTTCTTCCATGTTTTAAGAGGGAG
GTTGGGGTATACATAATGGCATATTGAATTGCCTTGTAACCCTCTCCGGA
GTCGATACTCTATATTCTCAAAGAAGATAAGCGGTACATGGGCAATACCT
GCAATTCGAGTTCGGTGAAAATGATGATCATGCCTCCGATAGATACGTCT
ATAGGGTGTCCAACCAATGCTTCTCATATCAAAATTATCGAACATACCTC
TATATACTTTTATAAGCTATATTATAAAGCGTGCAAATTTTTTAATCTTG
GTGGTTAATTGCTTAATTGACGGTTAAATATGAGTGTGTAGAACTTGGAA
AACTAATTTATTATTTTTAGAAAATGGGGAATTAACCTCTTAGATAATCT
CCAATGAAGTTGACTAAATTGGATTTTTAAGATATTATGTAAAATTTGTT
GAACATATAATACATTTTGTTTCGATGGTATATCTTATATTGATTGAATA
TATTTTAAATACAACATGTTATTATAATTTTAAGGATTTATAAATTTTGT
TTTAATATGATAATGGATCACATGATATTTGGCACAAAAATATAGTAATT
CGACCAATATAGTCATTCATCGGTTAAAATTATAGATAAAAATAAAAAAT
AGTTTTTTTTCTTCCGATATTTAAACTCATTTTTAGATAAAACTTCTTTC
ATGATCGTAATTATTCTTATAATTATCAAATAAACTATTTTCTAGTGTAT
TATATTTAGACACCAGTTCACTAAAACACTCGGTAAAAACGTTCTTATCA
TGTTCACATTCCAAAAAGATGTTTAAAATTTTATTAAAATTGAATATTTG
ATTATTTTGCCAAGTCTCGATTGAATTTTTGAGCAGGGAAACAGGATTTT
CTTGTCCGAGCCTACTAGAATCTAGCACCAATCAGCTAACAGTAACAAAA
ATCAGTATAGCTATCAGTCATATCACAATTCATCAAACAGAGATCAGTAT
AGCTATCAGTCATACAGACAACATTATTAGCATTTAAAATTTTTTACCGA
GCAGGGAAAAAGTTTTTTTTTAAGTCCGAGCCTACTAGAATCTAGCACCA
ATCAGCTAACAGTAACAAAAAGCACAATATTATTCTGGTAAGAAGAAGAT
AGAAAATAACAAAGAGCGACTCCATTTCTCTCCATTCAAATCTATTACTC
TTCTCTCGATTTCCCTTTCTTCTTTCATTTACTTTCTCTCTCACACTCTT
CCCACACACAAACACAATCCGTGTATTCATCTCCTTCCCCCATTCTCAAT
CCCCCATATCTTCATCTACTTCTTTACCCAGATCCCCAAATTCACAGATC
TACAAAACCCAGATCTCAATTTTTTTTAATCATGTCCGGATCAGATCTCG
CTCACAAAATCTTCCCAGAGCCTTGTAATATATTAAATGATGATATAGAC
CATTTTGATTCATTGCCTGACTCTATTTTGCTCCTCATTTTCAATCAGAT
CGCTGATGTTAAAGCTCTGGGTAGGTGTTGTCTCGTTTCGAAAAGGTTTC
ATTTTCTGGTTCCTCAGGTTGATAATATTCTTGTTCGTGTTGATTGTGTG
ATTTCTGATGATGATTCATCTGGGGGTTCTTCGTCTTCGAGCTCTGTGTC
GAAATCTCACACACCCTTTTCGTCGTTGTTTCGATTCGTGTTTGGTGGGA
TTGTGAAGCCTTTGCAATCGCTTACACAGTTTTTGCAGTTTAAGAGATCG
GTTAATGGGACTGGGTTTGCTGCTTCTTCGTCGTCGTTATCGGTTAATGG
GGAGGATTATGATGAATTGGATCAAGGGGGTGTTACCCATCATTCACCTA
CTCAGGTTTTGAAGAATTTTAATGAAATTAAGATATTAAGGATTGAGCTT
CCGAGCGGTGAGCTTGGAGTTGATGACGGGGTATTGTTGAAATGGAGGGC
TGATTTCGGGTCAACTCTTGATAATTGTGTGATTCTTGGAGCGTCTTCGG
TGATGCCTAGTAAGGGTTTGGATGGAAATGGTGTTAATTTGATTAATGAG
GATGATAATGGAAGTATACCTGAATCGTTTTATACGAATGGTGGATTGAA
ATTGAGAGTTGTTTGGACGATCAGTTCGTTGATTGCTGCTTCTGCTAGGC
ATTATTTGCTTCAACCAATTATATCCGAGCATAAGACTTTAGATAGTTTG
GTGTTGACGGATGGTGATGGACAAGGGGTGTTGTGTATGAATAGGGAGCA
GTTGGAGGAGTTGCGAGTGAAGCCTTTGTCGGCTTCTAGTGCTTCTAAGA
GGACCCTTGTGCCGGCTCTGAATATGAGGTTGTGGTATGCGCCACAATTG
GAGTTGCCGGATGGGACTGTGTTGAAGGGGGCAACTTTGGTTGCTATTAG
ACCAAGAGAACAATCAGTGGTGAAGAAAGAGGGGGCTGATGGGGCTTGGG
TGTCTTCTGCGTTTGAGGAGCCTTATGGAACAGCTGCAAAGATGTTCATT
AAAAGGAGGACTTATTGCCTTGAGATGAATTCTTTTTGATAGCACTCTGA
AGTTTCAATGAGGTAAATCCTTTCACATTATTCTTTGATTGACCGTATTA
AGTTATCATTTTTTGAACTTATGAATGAATTTTAGGCTTATTATCTGTAT
CCAATAGACATCAAGGTCAATTCTTGTCAACTTTGGCTCGTAGGTATGCA
GATTAATGTGGATTTTAGATCTCCGACACTGTCTGTGAATTTTCCTTTGC
CCTGTTTTTTCTGATGACCCATTCATGCTTGGTACTTGTGTGTTAAAATT
TCACTTTTTTGTTGTCTTTATTTTTTATAATCTGATTAACGTATGTCTGT
AAATGTACTTACCGTTGATGATGATCAATCAGTATGCCAGACACATTCCT
TTTTTGTAATGAGCTCTTAGTGGTGTAGTAAAAAATTACTTGTAACCAAA
ATGTAATGCACCGTGAAGGAATATTAGTCTGGCAGGCAGCACTCAGATTT
GAACCTGATAATCTTTTGAGTGTCATAAACTATACACCAGTAAGAATGCG
CACCCGATGCTAAAGATTGAGCAATTAGTTTTTTTTTTCTGTTGTCATGG
TTAGAAATGTAAGCTTGATGACCTATTTTGCAAAGTCTAGACTTTGTTTT
CCGTTCATGTGATTAGTGTTTGCTAAGTTTTTAATGTGTTTAATTAACTT
GCATGATCTTAATACTCTTATGTAATGCATTGGGCAGGGAAAGTATATTC
TTGAGATGATACGAACAATATATGTTTGTGGGCAGGCAGGTAATATACAC
AATTTTGCTCTATATCTTGCTTTATTTGAGGGGGTGTTCGTCAATGCCAA
ATGCTATCTTTCTTCTCCTATCTGGATGCAGCCAGCCAAACCTATCATCT
TTCTCTTATCTAAATGCCATTCCTTAGCCTGCTGACATCTGCCCCTTAAC
TGGTGAAGGTCTGAATGATGATGATATGCATCTGCTTCTTTTTTTATTTA
AGGCATGTGCAATGCACAAAATGCATCTAGATTGACATTGTACTAGCTTT
CCTGACTTTAAATTTGTAGCCAGTTGTTTACATTTCTTAGTATCCCTGTA
TATAAGTAGTTATGAATATGTTTGCCTCTATGATGCACCAATAAGCTTCA
ATTACTGATATACTTCACGATAAACGCTTTCCTGTTTAGGGCTAATTTAC
TGA