| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017367151.1, is a part of gene, LOC108199368. |
| The genetic_marker, MK009806 8_3917457, is located in gene, LOC108199368. |
| 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_017367151.1 | XM_017367151.1 | mRNA | DCARv2_Chr8:3914866..3920907 |
AGAAGAAAAGCATAGTCTGAAATATTTTCTCGTCCGATTCTAGCTGATTC
TGAAATTCGATTCTGACAGAAATGGAAGCTTCTCTCTGATCTATCACTTC
TTTCTGTAAAATAACCTTACAAATTCGAAGAAACCACACCAAAATTACAC
ATAATAAATACACACACAAGTACACAACTAAATAAATAAACAATCACCGA
TCATCATATTAGCGACTCAGAGTCTCTGTAAAAATGCTTCACAAGAGCTT
CAAACCCGCGAAATGGTAACAACTTCACTTGATTCAATATCTATCTGTAT
CTATACGTGTATGTATATGCTGATTTGATTTAAGTTAGGTTTTAATAACT
GATTGAATTTTTGAATTGTGACGTCAGCAAGACGTCGTTGAAATTGGCGA
CGGCGAGGATAAAGCTGATGAAGAACAAGAAAGGAGTGCAGATGAATCAG
ATGAAGAATGATCTGGCGGCGTTGCTGCAGTCCGGGCAGGATCGGACTGC
TCGTATTCGTGTACGATTCTTCGGTTTCATTTGATTATGATTATTTTCAT
AGAAATGCGATTTTTTTGTGGTTTAGTTGGGAATTATGTGATTAGAGTTG
GTAATTGATGTGTTTGTGTGGATGTAGTTGTGAATTGTTTGTGTTTTTGA
GGATCTGGAAGTTGTGCTTCGTTAAAACTGGAGTCTCGAGTTGAGATGGA
TGAGTGAATTGAATTTTTGTTGTCGTGTTCAGTCAAGTCAACTCATGTGT
ATAGATTATTTGTGATTACATATATTTGTTATTGTCGTTATTTTGTTATT
GTAGTCTTTATAATAATGATCTCGGTATCAATAGCTGGACAGTAGTATAA
TAAGTGTCGGTGTTTGCTTTAGTGAAGTTAAAAGTACATGTAAATTCAAT
ATGTTTTATAGGAAAAATTGGACGTTTGATTGATGGTTTTGGTTCTCCTA
ATGTCAAGTAAATGGTGGTTTGAAGGTTCTTACTTGCACGTAGTGTTGAC
ATCACCGACAAGTTTAGGAAAAGGTCATTTTTAAGTGTTTTATAAAGTGG
ATCAAGTAAGGTAAGTGGTTCAGCGCTTAGAAAGGTCATTTGCTGCATTT
GTCATTATTGTGTTTTGCACATTGTAGGAGCTTCAATGTACTTTTTATTT
GCAGTATGTATTTCATATTTCATTTAGGGCTTGAAAGCTTGATATGGAGT
TTGTATTGAGTCGAAGTCAGATGACTAATAATTTGCTTAATCTACAACAT
ATGTTCTCTTTCCTCTATGTTAGACATACTTTATGTTGAGCATCATTAAG
CTGTTACTGGAGTTATGTTGCACTTCCAGGTACCAGTACTAGAGAGAAGC
CTAAGACCTTAGTACTTGATGCATCTCTATAGAGTTTTATACTGATGCAC
TGATATCCCTGTTTAGCTCTTTTTTACTATAAAAGTGAAATTTATATTCA
TTTATTATCGCAATATAGAGGTGAGGATATATTTGGAAGCAAGTAGGAAC
CTAGTACCTTCTGTTTATTTACCACACATATTCTGACATCAACCAGATCA
TAAGTGTGCTTGTATCCATCCGAATTTTATTTAGCTTTTCTGGTCAGTTG
CCATCCAGTTTAGATGCGGCTAATTTTTTACATGACATTTAGTTTTTTAT
TTCATTTCTTGACATTAAAGCCCTATATTTTTTCGATGACAATGTTTTTT
TTTGGTATTCTTTGTCATAAACTGTTACTTTTACAGTCTCCTGAAACTGC
TTATATATTGACCTTCCAAATTCAGGTCGAACATTTCATCAGGGAAGAGA
AGATGGTGGCAGCTTATGATCTTATTGAGTTATATTGTGAGCTCATTGCT
GCACGCTTGCCAATTATAGAGTCTCAGAAGTATGTAAAATTTCATTATTT
TAGATGATATTGTACCTCTTTTTACCCTTTTATGGACAACTCTTATTTCA
GGAATGCAAATTTTTTGTTGAGATGTAATTTTCCCAAGAGGTTAACAATT
TTCATGAAATTGGAGAAATCAAAAGTAATTGTTCATAAGCCACTGATGGA
AACTTTCCTGCCATTTTATTTTTGTGAAAGTTCTGGCAGGTGTTTCTGTC
CATGATTTATTGGTTGTGAAGAAAACCAGTAGTTTTTGGCTTTCTGTAGG
TTCATTAAAAAAATACTAATAATAATCTTACTCTTTATTAATGTCCTTCA
TTGTTTGGTGTCAAAAGTCCTTCATTGTTTAAGTTTTTATGAAGATAGCT
ATTTTGAGGCTGCCTGGGTGGCTTTACTTTTGAATATGTTCTACTAAAAG
GGCTAGAACACAAATAAGATTTTGTAAGTCTTTTGACCCATATACAGCTT
TTGGTGGTCTGACTGTATAAACTCTCCTTTCTTAATACGAGAAATGCATA
ACTGCTTAAATACATTTTTAAAGTTGCAGAAACTTGATGTTTTCTTGTGG
ATGTTCATGTTTAATGAGTTGTTATAAATAATTTGTGAAGGAATTGCCCA
ATTGACTTGAAGGAAGCAATTGCAAGTGTGATATTTGCAGCACCAAGATG
TGCTGATGTACCAGAACTGTTGGATGTTAAAAAGCACTTCACAGCAAAAT
ATGGAAAAGAATTTGTTACAACAGCACTCGAGTTGCGTCCCAATTGTGGT
GTTGGCCGCATGGTAAGCTTCTATAGTTTGCATATCTCCTTGTCATATTT
GATCAAAAATCAACTGCTAAGTTGTACATAGTTCAACAGTATTGATGTTT
TTTGTAATCATGATATGCTTTCTTGTTTTCAGTTAGTTGAAAAATTATCT
GCTGTTGCACCAGATGGGCAGGCTAAATTTAAAATATTAAATGCCATAGC
AGAGGAACGCAACATCGAGTGGGATTCTAAATCATTTGAAGAAAAAGAAA
CAAAGCCAACAAATGATTTGTTGGTGAGCATGAATATCTGAAATACTGTT
GCATTTCTTATTTGTCATTTTTCCTGTATGAAGCTAGGTTTAAGTAAAAT
TGAGAACCCATTAAATCTCTTAAATACATGTGAAAATCTTTCGATGGTTG
ATGAAGTAATATCTGTCACTGAGCAGAATGGACCAAGTACTTTTGAGAAG
GCTGGTGAGATGGCAGTGGAAGCCACCAAAATCGGTGTTTCAGATGTCCA
AGCTACTTCTAGTCATGATAGGCACACCAGACCTTTGAATTCCACTGAGA
CAAACACGGTATCTTCGGTGGACGTGCACACTGTTTTGCCTGTAGATCAT
GGTGGTAGGAATACAAATGATATTACTCATTCTGATCCTAGACATTCAGG
TTCACCAGTTCCAATTTTACGCTGTTGATAAAAGTTACATTATTTATATA
TCTCAACTCATTTGGCAAATTTATATTTTATCTTATTTAGGAAATGAGAC
AAAGGTAGGCAGCCACTCTTTTGCCAGAGATGAAAATTATTCTAGGAGGC
AGGATTGGAATATGGAATTTAAGGATGCTAGGTCTGCAGCACAGGCAGCA
GCAGAGTCTGCTGAAAGAGCAAGTATGGCTGCAAGAGCTGCTGCAGAATT
TTCTAGAAGGGAAGATGATAGTAGGCATTTACCCTCTGAATCCAGGAACT
CAACTGGTAACAATACAAGACAAGATATGCCTGGGACATATTCTTCATCA
GAACTGCCAGGTGAAAATTTTGGAAATGTCCCTGTGAAGAACTCCTCCTT
TCATAGTGGAAATTCCAAGGTGCAGAATGATCAAATAGTGAGAGGTGAAA
ATCAAAATCGGGCAGAAGCTCGTGACAGATTGCAAATGTATGATCATGGC
AACACTAAAGAATCCAGTCATCCAACATCTGTGAGGCCTGGAGAATCTAC
AAGTGATGATATGAACTCCGTACATAGCATGCAAAGGCCACATGAGTACT
CTGGAAAAACTTCATTTGAAGAGACCACTAAACAAGTCAGGGAACCTTCA
GATTCTAGAACAGGGATGATGCAACAATACATAGAGTCCAGGGATGAAAG
TGCATCTAGATGGAAAGATGATTTCAGAGCTGAACATTTTGATCAATATG
GCGAAGGGAGACCTGAAAAGCAGGATCATCTCGGGTCATTTCACTCTCAT
TCCAGCACCGAAACTGATGATGTTGCCTACAAGGAATCAGGGAGTAATGC
TGCCCAGGATCTTTTTATCGTTAATGGCCAAGAGAGTATATACAGAGACA
CTACGAAGATGAACTCATTTGATGACAAATCTGTAGCTTTTGACGAATAT
GACTCCAGTGATGTCAGCCATAATCTGGATATAGGCCCGAGATATGATGA
AGGAGAGTCCACTACATATGTTTCACCACTAGGCAGTAATTCATCCTTTT
CATCAACTATAGATATCTGGAACCCTAGAAAAGACACAATCAAGTCGCCG
GAAAGAGCGACATTAAAACCACATCATTTTTCTGAATACCAACCCACTCC
TGTTTTCTCTGAAAGCACATCAAAATCTTTGGATCCTTTAGGACCAGACA
ATGTGTCTGTAACTCCTCATGATTTGGATGGACCAAAATTCGACAGCGAA
GATGAGGTGGAGATGTCTATTGATGAAGAAAAGAAAAATGTGTTATCCTT
AGATCCTGAGTCAGCACATGCTGAAAGTTATGACTCTACTGAAACTTTGT
TTGTGAACAGGAAGGATACTGATAATTATAGAAAGCCAGGTGTAGGATCC
TCGTCCGATGATGATTTGGTTACTATGGAAGCTCACCGACAGAGTGACTC
TATGATAGTTCTAAATGCAGACTCTCCAAAGTTTGATTCCGACAAGTATA
TGCAGAACATCAGCCAATCTTCAAATCTGTTGTCGACCCATACGGACGGG
GACAGATTTCTTATAACCGAGTCACCTGAGGCATTGAAAGATGAGGAATT
GAAACATCAGTCTGATTCAGAGGAAGAAGGTAAGCTTAAATTTGGAACCT
TGACAGGTGGGCTTCGCAATAAGGGCTACAGGCATCCACCCTCTATTAGG
AAACTAACAGGTGATTCATCATCGAGGAACCCAAAAACTACAGATGAGAG
TTTAATGAAAATTGAGCAGCAAATTTCCCCAATCTCTTTGGAGAGCTCTG
TGATTGCTACACTGAGCAATGATGCAAACACAAAATCAAGCTTTAGCACA
TCAACTCTTCATTCAGATTCTGATTCACAGACTGATGATTCTGGGGATGA
AGCCCAACAAAATACCATCAAGGGAAGGCAAGCTTCGCTTGGCAAGAAGC
CCAACAAAGAAGTAAAATATAAATCCAGCTTCAGGCCTCCTGTTGCCACA
TACTTTGACCTTGATAATGAAGATTACAATGACGATGTCCCGAAACAAAA
TTTACCCAACAAGGGCCACTTGGGAAGTGCAATATCTCGCAGGACAAAAC
CTTCACCTTCAGGCCCTGGAACCAAATCATACTCCAAGATTCAAGCTGAG
CATGAGGAATCAGCTAAGCCAAATCCCAGTAAAGATCGAACATCCACTAG
AGACCGCCCAAGTAATGAAATACCAACCAAGATGAAGTCAGAGGTGAAAA
GTGTCGACTACTTTTATAGAGAAGAACAGCTGAACCCTGCAAAATCCGAA
GCTTCCAAGTCTACAGTTTCCAGAATCCCTCCCCATGAGAGACCTTTAAA
CTCATCAACAGCAGAAGAATCTTCCAGCGGTCTTCAAAAAACAGAAGCTT
CAAGTAGCCTACAAAATCCAAAGACATTGAAATTTACAGGGGAGCCACCA
ACAAGGGAAGATTCCACGAAGAGAGCGAGTCATGTTCATCCAAAACTTCC
AGACTACGACTCCATAGCTTCTCGCTTACAATTATTGCGAAAGGATCAGC
AGTAAAGATATACAACTACACTACATTATGATAGCCTGATCAGTGTGTAT
AGCCTAGTAAATAATATATCCTTGGTTTGCAAAGCTTGTGTAAAGTCTCA
TATTTGATTTGTTGTTTCATTTGCCGAAAATGAGTAATTTTGTCATGTAA
AAGACATTTCACTAAAAAAAATCTCCTAAAAATTTGATAAA