| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017381873.1, is a part of gene, LOC108210545. |
| The genetic_marker, MK004553 K1997, is located in gene, LOC108210545. |
| The mRNA, XM_017381874.1, is a part of gene, LOC108210545. |
| The mRNA, XM_017381872.1, is a part of gene, LOC108210545. |
| The mRNA, XM_017381871.1, is a part of gene, LOC108210545. |
| 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_017381871.1 | XM_017381871.1 | mRNA | DCARv2_Chr3:31315515..31321647 |
| XM_017381872.1 | XM_017381872.1 | mRNA | DCARv2_Chr3:31315515..31321647 |
| XM_017381874.1 | XM_017381874.1 | mRNA | DCARv2_Chr3:31315515..31321647 |
| XM_017381873.1 | XM_017381873.1 | mRNA | DCARv2_Chr3:31315515..31321647 |
GCCCTTATTTCCACATCGTAGCAGACTAGCAGCAGGCCAGCCGAGCAAGT
ACTAAAATATTATTATTCATAATATATTTATTGTATTTTTTGCTTTTTGG
TGGGTTTGTTAGAAAGAATAATCGCCCAAAACAACGCCACCAAATTTAAT
GCTTTCTCGAACTCTTCTTCTTTATATAAAACCGTGTTTTCTAAGTAAAC
TTTGCATTTTTTAACAAGACTCCAGTCAGCACAATTCACAAACCCTTTTG
ATTCAACCACAAGCTTTGATTTCTTAGTTTAAAAAGGTATGATATTTAGT
ATTAATATAATGAACTGATTAATGGGTCTGTTTTAGATTTGTGTATTTAT
ATCAGGGTTTTTTTTCTGTTGTTTAGATTGTGTTCTTGATTTGTTCTATG
ATGCTTCTGATTGTTAGTGAAGAACAAGATTTTATTATATTATTTCTCTC
CTTTTGGTGATTATGAGATGATCGATTGTAGAATTCAAGAATGGTGATTT
GCTTCTTCTGAGATTTTTGCTGTTGTAAGTGTTGACTTTTGTTGACTTGA
CTTTGATCATTTGCTAATTGCTATAGCCTATATTAGAAGTTTGTTTGTAG
TATTCATGCCATTTTGTTGGGTTTTTGTTGTAAATTGTCTCTATCATTGT
TGCAGTGTAAAGGAATTCTTGTTTACATGTTACAAACATCTTCATGAAAT
TTCTGTATTGAAATTTCTTTTGAGATATTCCCATATGAATGTCATTACGA
TTTACGAGATAAAGGTTACTAATATTGTTTATATAGTACTTACTTGTATA
TTTGATAATCCGCACCAAAGCCTTCTTAAGTTAGTTGTAATCTGGCCTGC
TATCCACGAAATTCTGTAAAGTTTGAATAATTCTATTATTGCTGCGTCTT
ATAATGCAGTGATGATTTTTACGAAAGATAAGATCACTGTGAAATACTAA
GTTACTAACAAAATGAATTCTGGTGGAATTATCTACAAAGGTTTTGTCAT
TGCTGCTCTTATGGGTGAACATGTAAGTTTCTCGCAAGTTTAGATATATT
CATTGAGGTTAAATAGGAAATTTTCTCATTTACAGCTTCTCTTGGGGCTT
CATCAAATTTTGAAGTGAAATACTAATTAGAAAATGTAAGGCTTATTATA
TTTTAGATCGTAATAGAAAAACACAAATGAAGACTTTGATTTGGTTTATA
TTCTAATTATTTTACATATACTTTAGCTGTGTTTGCTGAAACCATTTAGC
ATGAGTTTAAAGCAAATGAAGTGCGGAGTGACATAGGTAAATTATCAAAT
GTCCAAGTTGCTCACTGTTTTTGCTAGTACGACAGCAAGCTGAGACTTGC
AGAAAGGAGTCAGCCATGTATGATGTGTCTTTTGAAAATAATTATATGAT
TGCAGGATGTTGATTCCCTTAAAAAAATGAAACTAATATGAGCGGAGAGG
CTTGAGAGTAATAGTCATGACTGCTAATTTTAATTTATGATCGGAACCAA
ATGATTTTTGTAATAGATTACTAACTGAGAGTAATCACTACTCATAATAA
TGACCTTCAAGTCATAACTCACACAGGTGCTGTTCACTGTGAGATTATGG
TTTTTGTGCACATTCAATGGTTTATCTCATGTATTTTCACAGTGGATATG
AACTATATGTGTTCGTAAAACTTACACGAATATTTTAATCGTTCATCATT
TCTCTTTAGACTGCTCATGTCATTATTATTCTTTCTAGTGAGTTTGCGGC
CTCCATGCAAGATGTTCAAATTGCCACTGTCTAAAAAAAGCCCTTAGAAT
GGTTCAGAGATCTGCTTTAGTCATTATCGGGGTTTCCGTCGGTGTTGCTG
TTGGAGTTGTTGTAGCTTCTCTGGTCTATTTTGGCATACGGTGGTTCAGA
AAGCATGCTAATCTGCAGCAACAAGCAAATGAACGATCCTTGTCAACTCT
TCCTATACGTAGGAATGGTCAGGACAAGAGCTTTGACTCAAGTGCATCAT
TCTCTGATTCTGTTACTGTTAAGATTATAGATCATCCTGCACAAAAATCT
CAGCATTTGTGGTGGAGTCACCATAGCAAGGATAAGATTGCTCCCACAAG
TGGTATACCTAGATACCCTTACAAGTATGTTTATCTCTGATCTCAAAGTG
AAGACAAGTTTTAGTCTATTGGTTTTTATTTGTAATTCTGATGGCCTGAT
TGAACATCCCTTTGTTCTTGGTAATGTATCTCGACTTCAAATACTAAAAA
TGTTATATCATAGAAAATGAATATGATGTGAGTTATGACATGGTGTCTGG
TTGTGGCTAATCATTGTCCTGTGTCCACCAGTGACCAGAGTGTCACCTAA
AATTTTTGTGCGCACTCAACAGTGTATAAGCACAGATTATCTTATTGAAC
TTAACAGGACTTACGAGTTCCGTCTATAAATAGCTTCCTTTTCTTTCGTT
CCATATTTATAATTTTGTTTAAACAAGTAATAACATTGAAAGTTTATTCA
GGGATATCCAGAAAGCTACGCAGAACTTTACAACTATCCTGGGGCAGGGA
GCCTTTGGCCCAGTGTATAAAGCAAAAATGCCTTCTGGGGAGATGGTTGC
TGTCAAGGTGCTTGCCTCTGATTCGAGACAAGGAGAAAAAGAATTTCAAA
CTGAGGTAAAGGCTAGATATTGGACTTGTATATTTTTTTTCGTTTGGTTT
AGTTCAATATATTCAACATTAACTTTATGTGAATACTTTTTTTTAATATT
TAGGCTTATATGCCTTAGAAATGAGGGCTGAGCGAGAATCGAACCCAGGT
ATCCCAGGACGACAGAGGATAAACCCGCAACTTGGGCTATCCAGTCACGC
TCATTTTATGTTAATATTTTGTATCTTAAACATGTACATTAAGCTTACAA
TATAACATACAGTCTCTGGAATATACCTCATGTTAAACTCAAGGTTGAGA
TAGAATATGTCCTTGAGAAATTTTATGTGAATGCTTTGTGTCTTAAACAT
GTACATTTAGCTTACAATATAACATACAGTCTCTGGAATATAACTCATGT
TAGAGTCAAGGTTGAGATAAAATATGTCCTTGAGAAGGGCAAAAATTTTG
AAATTTATATTTCACCTTAAAAACGAAACAGCAATTGTAATTCTGAGTTG
ATATTGGTTTTAGCACAACAGTTTAGGGATAAAAATATATGGGTAATAAA
GCAGCTGAGGAGGGTTGCACAGGAGGGTCCATGTAGAAGCAACAAATTAA
TGTAAAGCTATAGTTATCCAATTCTTTTCTTGTATTATGAACCCCAATTT
TGTACCTTGTATAATTTCTGAAGATTGTTTCCTTATTACTGTGTGGCTCC
ATTTTCCTATAGAGTATCCTCTGTGTGAATCTTATTTGTGTAATCAACTA
AGATAGTTGGCCTAATCTATCTGCAGGTCTCTCTACTTGGTAGACTGCAT
CACAGGAATTTGGTGAACTTGGTTGGATATTGTGTAGATAAAGGGGCACA
CATGTTGATTTATGAGTTCATGAGTAGTGGTAGTCTGGCAACCTTTTTAT
ATGGTTAGTTGCGGCATGCACTTCCCTATTTTCAAAGTATTATTCCTTTA
GGAGCTTCCGAACTGCCTAATAATTGGAAAGCAATGAAGACTTGGTTACT
TGCTTTCAAAACATGTTTGACAGATTTGCTTTTCCTTAAGTAATATATCT
GGTAATTCGTTTGTATGCAGTAGTATCACTGCTGATCTGCAAGAGTTATA
TAAATTAAGAGCCACAACATAACAATGTCATATGATGCCATGAGCGCTTG
AGCAAATAACTCATTGCTTAGATTCTTAATGCACAATTTTGTCAGACATG
CCAAATCTCGGGGTCTTTTCATCATACCTTCTGATTATTTAATACAGTAC
TGCATTAAGATTTCTTTCTGCCAAGGGTTTGATCAAATGTTTTGATTTTC
CTGATCTGAAACACTTAGATGAGGAGAAGAGAACTTTGAACTGGGAAGAA
CGGTTGCAAATTGCACTTGACATTTCTCATGGGCTCGAATATCTTCATGA
CGGGGTAAGCACATTAAGCATCAAGATATTCAGCTTAAGTAAGGACATAT
ATTATTAAGAATATTAATTTTAGCTTTTTTGAACAGGCAGTCCCAGCTGT
CATACACCGTGATTTGAAGTCTGCTAATATATTATTGGACAATTTGTATA
GAGCAAAGGTAAATAATTTGCACCATCCACAGTTGTTTAATTACATTGCG
TGATCCCTGTCTAGATGATTTAATGGAAACCAGGATGTATAGTTGAGGAA
ACAATTGATTAAAGTGTAAAGCAGAAGGGTCTCGGGTGCTTAAGTGTATG
CTTTGTCGAAAAGAACACGAGAAAATACAACCCGTATACGTATATTTAAT
GACTATTATACTATATAGTAATTAAGAAGAAACAACATTGTACATTACAA
ACAGGTTCAAATAGTCTAGTCAATAATATACAACTTGCTTTGTCAAAAGG
AAGCACACTAAAAACCTCAACCCATACATGTATATTTAATGACTCTTATA
CTATATAGGGAGTAGTAATTAAGAAGAAACAACAGTGTACAGTACAAACA
GGTTCAAGTAGTCTAGTCAACAATATACAACTTGTTTTTATATAATACAG
GAAGCACAAGTACATCTAACATATAATTGTTTTCATTTTTCAACCATTAT
CTTTTTCTTAGAAAATTCTCAAAATCTTCGCCGCGGTTCATCTTTCTACT
TATTATGGTTTAAATTGATGTTAGAACTTCACATGTAAGCCCCTTTTTAA
ATGTGTGGTATAAGCTTTTGGCGCTTAGCCAGCGCTTCTTAGAAGTGGCT
AGGATTTCTCAAAGCAAAGCGGAAACTTGGCACTTAACTGAGTTTTCGGC
TTAATCAGGCTCTTAAACATGCTCTCCACATCTCTGTTTAAATATTGTTT
TGTAAACCTGATAAGATCAGTAAATGTCTGCAGAGTACGTCTGTCTTATT
ATTAAGAAATGGTGAGTAAGTTTACCCAGTATGAACCTAGAATATGCACA
GATAAATTCTGGTTTTCTTTACTAGCATCCTAACATTTACAGTCATCCCT
TTCAAACAGGTTGCTGATTTTGGGCTGTCGAAGGAAGAGAAATTTGGTCG
CAGTAATTCAGGCCTTAAAGGAACTTATGGTTACATTGATCCTACGTACA
TATCAACAAACAAGTTCACAGCAAAGAGTGACATTTATAGTTTTGGAATC
ATACTCTATGAACTCATTACAGCCATCCATCCACACCAAAACTTGATGGA
ATACATTAATCTGGTAAGAAACTATTTTAACAAATCCTGTGTATTATTCT
GCAATTGTACCAAATGATCGTTGGACATTATAAATTTTTTCTCCTTTCAC
TAAAGGCCGCCATGAGTTCAGACGGCATTGATGAAATTCTTGATAAACGA
CTGGTTGGAACATGTAATGTTGAAGAAGTGCGTAGCCTCGCTCACATTGC
CCATAAATGCTTGCACAGCACACCCAGGAAACGCCCCTCAGTTGGGGAGG
TTATGCAGGCAATATCTAAAATCAAACAGAGGCACATGGGTAAAAAAAAT
GTGTTGTCATTATCAGAAGACGATTTTTCAAGTGTGGTTAGCCGAATAGA
GTCGCAACACATAGAAATGGGTAGACTAACCAGCATAGCTGAGAGAGCTT
AAAAGATCCCTTATAAGTTATTTTTATTTTTGTAACTTGTACAACAGATG
CATATATGATGCATATATGGTAGTAGCCTGAAGATCTTGTCATCCCAGTT
TTATGTTTGAGGCCAGTAAACCCACTTACTCCCGAATTTCATTTTATAAG
GGAAATCAAGTAATTAGTGGTTTAGCGTGAGTAGAATTTTTTTGCTCCTA
ATGGTAATCTTAGGAGTATTTAGCGGCGGTTGATCATTAAGATATAGGCT
TGCTTTCCAAAGTTATGCTCTTATTTTGGTGGGGGTTTTTTTTCACTTGC
TTTTCTTTTACAATGATGCAAGGCTCAGGAGTGTGTATTTATTCAATGTT
GTCTTTGTGATTGTAATTGTACTCCATGGAACAGGTTGATATTTTTTTCC
CTGAATCAAAATTTGGGTATGGGGTTTTTGAA