| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017386869.1, is a part of gene, LOC108214713. |
| The genetic_marker, MK002712 K0156, is located in gene, LOC108214713. |
| The genetic_marker, MK002139 ESSR-034, is located in gene, LOC108214713. |
| 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_017386869.1 | XM_017386869.1 | mRNA | DCARv2_Chr3:10467653..10475640 |
AAGTATATACTAATGTATACACACACTCTAATACAGTAATATATTCTACA
TACATACATATTCGTAGTTCGAAGCTCCTCTGCAACATTCTACAAGTCGT
CTCCGCTGACTCTTTTTTTTCTCTCTCTCTGGTAATGCACTTAAGCTTGA
TTAAAATGATGAATTCTTCACTAATTGTAGTCTCCGCTAATTTTCCTCGT
TAATTACCTTAACTTGATGATTAAACTCATACTTCACCTTTTTACAAGTC
ATTATAGTCATTTTTTTGGTATTTAATCATCCCCTTTTTTTTGTGAGAAT
TTGAAGATTATATTTATGTATATTGCTGTTTGGTTTTGTATCAATTGCCT
ATGCTGGGAATGATAAGTGCCCTTTTTGTTGTTTTTGTATTGTAATCACA
AGTTCTGATTGTCTTTTTTTTCAGTTGTGCTAATTTACAAACCATTGGGT
GATATTTAGTGATGAGTTGTGATGATATTGATATGTCTGATCATTCATCG
TGGCTTCTTTTGTTTCTTTTTTCCGTTTGTCTTTAATAATGCATATAATT
TGCTTTTTTTAGAGTTGTGTACTTGCGTTTTGTTGTTGAATTTTCGAGAA
TTTGATCAAACAAAGTGGTTTGCTGTGGTTCCAGTAAATGGGTGCACAAA
GATCTCATATGAGTAACCTCAACCTTGTATATATCTTTCTGGAGTTGATC
CTGATCTTTGAAGCTGGAACTTCATATGGCTTCACTAATCCCGTTGATGG
TGAGTCTAGTCCTGTACCATTTGCGCATTTGTGATATATTCTTTGCTGAT
TTCGGATTTTATTACAAAAAGATCAAAGAACTTCATGAATAGCTAAAATA
TATATATATATATATATATATATATATATATATATATATATATATAAAAA
AATATCTCGATAGTCTCCTGTTATGTTTGCTGTTTGCATATAAGTATAGA
TATTTTTTGGTTCATATTTGCTGACTTTTCACCTTCACTTGCTTAATGAC
ATGAATATTGTATTAACGTATTCTGCAATACATTTACATTGAAACAGTTG
CTGCTATTAATAGTTTATATATTGCGGTGGGTTCCCCTATTCTTCCTCGC
TGGACTTCTGTTGGCGGAGACCCGTGTGGTGATGCTTGGCAAGGTGTTGA
ATGTGATGGATCAAACATAAGCTCAATGTATGAACTAACTTGAATGTGTC
CCCTTTAATCATGGTAAATGTGTGTGCTGGACCTTTTATCAATCCTCTAA
CATATATATAATGTTCTAGAAAATATAATGTTGCTAATATGAACGGAGAC
CTGGGCGACAACTTGGGATCATTTGCTTCCATCAAAATAATGTAAGGGAT
CCCTCAGCTCATTTGCACAGCGTGCCTGCTTGTAATTTATGCATTTCTGT
TTTCTAGTAGTGCACAAAATGTTTTTGAACTTTATGTTAATGTTTGGGAC
TCAAACATGTCTCAATATCTTTAAAGTTTAATCAGTAGGTCTTTACCCAG
ACTTACCTGAGAATGCTTAAAATCTTCACTTAGGTGAACTGACTTCTATA
GAATTCCAAAATTCTGTAATTTAATCTTCATTTACTATGCCCAAACACTT
TTCTATATGAAGTTGGTTAATTCCTTAGCATATGAACCTCATCTAATTGG
AAGTTTGTCAGACCATTGGTTTTACCATCGCAATTTATTTAATTTCACAT
TTTCTCTCGAGAGTTATTAGGTATAAAATCTTTTTTCAGTTGTAGTTAAT
GGTTATGACAATTTGGTTTTTCGACAGCGATTTGAGCAACAACCAGATTG
GTGGGACTATCCCAACAAATCTTCCCGTCTCCCTGCAACAACTGTATGTT
CTTTTACGTTCCTTGCAAAGAGATGCAAATATTCCAATTATAATCATCCT
AGTAAAAAATAGCTTAGTTCTGATGTCTGAATATATTGCAATAGCCAATA
GCTTTGTTCTGACTTCTGATAATATAGTACAAGTCCTATCACTTGAAGAG
AATAACTTATTCAAAAGACTTATCAAATACATTATCTTTGTAAGTTCATA
TAGATTTTGTCATGGGACAATGACCTGCTAATATGACTAATAGATGCAAT
AACATATGATACCTTACCTTTGGCAGTTATCTAGCAGATAACAAGTTCAC
CGGGAGCATCCCTGATTCTTTGTCATCCATGAATCAGTTGTCAGCCATGT
AAGTCTTTTCGCCACCTTCCCCACCCCTGCAAGTGCCAGTTGCTCATGTT
TGCTGGCTTCTTAGCTTCTTTAGTTATATTTTCTTTCTTCTTCTTGTCTT
AGGTCTCTAAATGGCAACCAGTTGACAGGAGACATACCAGATTCCTTTCA
GGGCCTAACTGTTTTGGTGAACCTGTAAATTCGTGAACTAAAATTTGTTA
TTTTGTAAGATTATTCTACTAGTGCTTTATTCATGAATACCTTGTCTCCT
GCAGAGATTTGTCCAGTAACAAATTGACTGGACAATTACCACCTTCCTTG
GAAGGTCTCTCATCTTTGACTACCTTGTGAGTGATTATCAAACATCCCAA
GATTAAGGTTGCTTTTCTGTACACTTCATTTACATGAATACTAAGTTTTT
AACTGGCAGCCGTCTGCAAAACAATCAGCTTTCTGGGACACTTGATGTTC
TCCAAGATCTTCCCCTCAGAGATTTGTACTCTTCTTAACCATTTTGGTTT
TGTAGCTACTATTGTTTAACTGCTTTTATAGTTTGTGTTTACTTTGGTTA
TATAGATTCTTATATTGTAATGAATTTCAAACAAATTGCTGAGGTATTTC
CTTTGTTAATTTCTTCTCAGGAATGTAGAGAACAACAGTTTTTCAGGACC
TATACCTGAGAAGTTGTTAAGCATTGCCATTTTCAAGTGAGAACTACACT
GTTTCTTCTTTAACTTACTTTATTAGGTCATTTTATTGGCTGTTTTATGA
AGGAACGAATTATCATTCTGTCAATTCCTTAGAACACTGACATGTTTATA
TGCTTTGAATCCCCTGATACAAATTATAATAAAAGAACTTATCAGAAATA
ATAGTTACTGACATGTTTATGTGAGTTTTCCAACAAGGGTATGTAATAGT
AACTTAGAAAACAAAGGCCTGAATCTGTAATGGATTATTTAACCCAGTGA
ACATCAGAAGTTGCGACAATGATAAATTCTTTAATGTTGAAATTAATATA
GTGCGATTCAGTTTCATGTTCATTCAGTGTTGGAAAACAATTTGTTAAGA
TAACTCAGGTCTCAGCTGTCTACTAGAGGAAGTCCGTACTCAGTTTTGTG
CTCGAATAGTACTGATAACTGTCTTTGTAACTTAGTATGCCTCTTCATCT
TTGGATATAGGTTATGGATTAAAGGACCAGATTCGTGCACGTGCACGCGC
CCACACATTTATATATTAGCTGGACCTATATATAGTAAATTAATCTCTTT
ATAAGTATCTTTGCACTTCTTTTTGATAAAAAACCATGCTTATCCAAGCT
TAGCTTAACGTCTACAGTCCTTAAGTTGAGGTCCAATACTATTGTACTTA
GTATCTCGTAAACTACTGTTATCTGTTCTGTTGCTCGATTAAGATTATAC
TCTGACTTAACGCGCAACTGCCTTCCTGGGTTTGCAATCTGAAGTCGTGG
GATATTTTCTAGTGAAAATAAAAAATCATTGTGACACATAGGCAGTACTT
TTAGCTGATTTACTTCTGTAGTAACACATAGAGGTATATTAGTTTCAAAT
GTGTAAATCTACCTGCAAGTCTGTACATAAACACTTAGGTTTTCATGATT
TCCTGACTATGGGTTGGGTGACAATGGCGTATGGTATTGACTGCAGCACC
ACATTGTCAAGATACATTCAGTGTGGCAGCCATACAACTTGATTGTTGCT
AAACATAATAACTTTTGCAGATCTGATGGAAATCCGTTCAACACTAGTGT
TGCTCCGAGTGCCCCGCCAACATCGCCAACAGGCTCGCCCACATTGCCAA
CAGCACGTCCACCTGCTCCACCATTCTTTAGAGTTCCGGCCTCTGGGCAA
ACACCGGAGAAGGCACCTGGAAATGAAACACCAAGTAGACCAGCCGATGG
ACCATCTGCAACTACGGATGCAAATTCAAAAAAGACTAATCAAAGTTCAA
ATACCAAGAAAATAGTCTGGATATCAATTGGTTCTGTTTTTTCGGTTGTT
ATTTTATTGTTATTACTAGTGCTTCTTATCCCAAGGTGTTGCAAAGAGAG
AGGTGACAGGGTTCCCAGGCGGTATGAGATAGCTCCATATATTGGCAACA
GAGAGAATCTTAGAGAATATGGATCCTTGGAACAACCATTTCATCAGACA
GAAAAAGGTCTTAAGTTTTATTGGTTTTTATCCACTTGTATATAATGAAA
TTTGTGACTAGTTATCCTGAATATTAATGCCTTGAATTTAATTTCCAGGA
CCCAAGGTGGATTTAGTTAAACCCCAGGACAATTATCTAAAAGGACCGAT
AGTGTCAAGTTTAGCTCCAATGCCGAGAGAGGAGCTAAATGTTGATAAAA
TGAGTGCAGTACCAAAGGTTGAGGACCATGAGATTGATATGACCAGATTT
GATTTTGACTCAATGTTGCCACCACCACCACCACCACCTCCCCCTCCATC
TCCACCGCCACAGCTAGCCCCTCCAGCACCTCCACCAATGCCATTAAAAA
GTGTCACTGTGAATCCAATTTTGCCAGCTCAGACTATTCCTGTAAATTCT
TCGTCTGGACCTCTGCCTCCAACAACTGTACGGTCATACTCTATAGCATC
CCTTCAGCAATATACAAATAGCTTTTCTCAAGAAAATCTCATCGGAGGAG
GAATGCTGGGAAATGTTTACACAGCACAGCTTCCTAATGGAAAGGTCCAC
AAGAAATAAGTCTTCCAACTACTTTTAAGTCTTTTTAACAGTTTATTAAA
AAAAGTACCCCCTCCGTCCCATCCAATTTTTTACATCTGGGAGGGAGGGA
GGACTTGGCAATGCATTTTAAGGCTCGTATAAAGTATAGTTCCATAACTT
ATTTTCAAAATTTTCTTTTTCTGAATATAAATCAAAATATTAAACTTTTA
TTGAGAAAAAGAAAATTTTAAAAATAAGTTATGGAATTATACTTTATTGG
AGCATTAAAATGTGTGCCGAGCCCTCCATTCCAAACGTAAACAATTGGAT
GGGACGGAAGGAGTAGTAATTAGTGAAGAAATGCAACTTGGGTGTAGATG
GGTAGTATTCTGAGAGCATCTGAACTTGTGTAACATAGAATACTCGCATA
GTTGTCCTCTTCGTATGACATGAGCATATTAGTACATATAATACATCAGA
TACTTGGTTGAGTTGTTCTTTTTTAAAAATTGCACAGAAGTTACTGCATT
AGTTGATCGAAATATCACTTGTATCAGCATCTACTTTTTTTATGAATACT
CTATCTCCCTCTCACAGACATGTGAGTGTTGTGACCTGGATGATAATGAT
AATTGCGTGTTTTGACATTCATGTTGTTGGGTGTATCTGCAGCTAGTTGC
TGTCAAGAAGCTGGATAGAAGGGTTTCTAGTCAGCTAAAAGATGATAAGT
TTCTTGACCTGGTAAACAGTATTGATAAAATTCGTCACGCCAATGTTGTT
GAAATTTTGGGTTATTGTGCGGAACATGGCCAAAGACTTCTGGTTTATGA
GTACTGCAGTAATGGGACACTTCAAGATGCACTACTTGCCGATGATGAGT
CAAAACCTTCATGGAATCTTCGAATTAGGATGGCACTCGGAGCTGCGAGA
GCTTTGCAGTAAGTATAGCAACCAAATTTACACACTTCACTAATTTACTG
TATATCCATGTTACAATGTTTGGGATTTTTAACTTGACCATTATCTGCCT
ATAAGGATAGAATTACCTTCAGTAGTGTTTCTATGCACGAGTGCAGAATA
TAGGGAGAAACAACGGACGTAGAGTTATATGTTTATCAGCTTATAATGGA
AGAGTCCTTTAAGTTTCCTTCAACATTTATACTTGTGGCATCACAAATTT
CTATCTGCAACCTGGAGAGCTATCTGTTCTAAATTATTCTGCTAATGTTG
ATCCTACTTCTTCAGAAACTAAAATAGTATCATAGGCGAAGTATGGTAAA
TAATGTTGATCCTACTTCTTCAGAAACTAAAATAGTATCATAGGCTAAGT
ATGGTAAATAAAATTTATGTAAGAAGGAAGGGAATGGATTCCACGTGTCT
CTGATGTATAAAATGGTCCCTGTTGACTCTTTGAAGTTATTTGCCAAACC
CTAAAACATTATATGTTAGAGGCTTAGAGGACAGTATTTTATCATCAAAC
ATCCAATCCAATCAATCGAAATTTTGAATAAGAAATTCGTGAGTCGACTT
TAAATAGGGAATGGTGCTCTTATGTGATAGTATTAGAGAAGTAAAATACC
AGAAAGGTAATGATAGAGTAAATTTGATGATATAGTTCAGAGATAAAAAA
GGGTAAAATAAAATCTTGAGAGGCCAAAAAATTAGACTTCTGTAAACATC
TGTTATGCATTGTTTATTAAACTACTATTTGATTTTTATGATGAAGGTAT
TTGCATGAGTTCTGTGAGCCACCTGTTGTTCACAGAAACTTTAAGTCTTC
TAATGTTCTCCTTGACGATGAGCTTACAGTGCATGTATCAGATTGTGGTT
TGGCACCTCTAATATCATCAGGCTCAGTCAGTCAGGTACAAATATATTTT
AGCTTATTAAATTCTTCTCTTGCTTTTGAAGCTTTAAAACTACATATGTT
TTGGTATTGAGTAGTCAAATGATTGAAAAGTAAAGACATCTACCTGTGTC
ATGTTCCTCTGCAGCTGTCAGGAAACCTACTTAGCACCTACGGTTATGGT
GCTCCTGAATTTGAGTCTGGGATATATACTTCTATGAGTGATGTATACAG
TTTTGGAGTCGTGATGTTGGAACTCTTAACGGGAAGAAAGTCACATGACA
GGTAGAGCTACGCATTGAAGCAAATCTAGTTTATAATTTTATATTTAACT
TCCTTTGGCAACAGTCTAATCTCTGACTGAATATTGTGTTCAGCACACGG
AGCCGTACAGAGCAGTTTCTTGCAAGATGGGCAATTCCTCAGCTTCATGA
TATTGATGCATTGTCAAGGATGGTTGATCCTTCATTACAAGGAAAATACC
CTGTTAAATCATTATCCCGTTTTGCTGACATTATATTTCGCTGTGTTCAG
GTATATTCTTCATTCCTGAAAAAATGTTAATATCTTAAAAGAGTTGGCTG
GTCTTGTTGTGGGAGAGTCTAAAATTTGAATGTCTTTGTATTCCAGGAAT
GAAATTATTTTCGCTAACCTTACGTACCTCCAGTAATGTAGAGTTGCTAA
TATTGCTATAAAACGAACCCTTCCCCTGTACACAGGCTGCTAATAATTGC
TTCTATATTCTTAGTATAGGCAAGATTGACAATAATGTTTCATACTGCAA
CAATAATATTTATTTGTAGAAAATTAGATCTTTCAGTTACCCCACCACCA
CCTCTCTTAAACATTTTCTTCACTGTACCATGTTTTAATATTGCAGCCAG
AGCCAGAATTCAGACCACTGATGTCTGAAGTTGTCCAGGATCTCCTACAA
CTTATAAGAAGAGATTTCGATTAAGCCTTAGAATTCAAGTACATTGGTGG
TAAAGATACACACTTATAATTCATGAATTGCAACTTTGAGAGGGCACATC
AGCGAAAATTGGCCTTGCTAGATCCGTAAACAAACATCAAATTCATTCAT
TAAAGGAGCCTACCACGCATGCAAGGCTATGGCATTCAGCTTCAGAAACT
TTCTGGCAATCAAGTCTACATGTTCTTGTGGTAATTGTTTACTATAATCA
ATTTCATGTAAGATATCCACTAACCCATTTCTTTGTAAATTTTTATTTAT
AATCAAATCTTGATAGTGAAAGAGAATATTCAGAGTA