| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017364119.1, is a part of gene, LOC108196713. |
| The genetic_marker, MK009696 7_5492146, is located in gene, LOC108196713. |
| The genetic_marker, MK003085 K0529, is located in gene, LOC108196713. |
| 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_017364119.1 | XM_017364119.1 | mRNA | DCARv2_Chr7:5491587..5498041 |
AATAATGTAGTAGGAGGGTTACTCATCTGGAAAGACGGTGAGTAGTCAAC
AACCACTCTGTAGCTGCTTACCTGTCATTATCATCATCAATCTACACATA
CACACATAATTCAATCACAATCACTACTTACATTTCACTGTATCTATATT
TTTACACATCTTTCGGTTTTTCAATATTTTCCAAAAGCGTGAGCTCCATC
TCACTGAACAAGTCTCGTAACAATAAACAGCAAATATTATTTTATTATTA
TTTTAATTGAATTTTTGTCAAACTGAGCTGAATTGACGGAGATGATGGAA
GGGGAAGGGGGAGGAATGAAGGCGGCGATAGGAGTGAGAGCGATGGAATC
GTTAGGGTTAGGGTTTGATTTAGCGAGTGATTTTAGGTTGAAGTTTGCGA
AGAAGTGTCCGGATTCTGCGGATGGGAGATTGGTGGTTTTGGATGATAGT
AGTCGGAGAGATGTTGTGCTTCCTGGCGGCGGCGGCGGTGTTATTCGGAA
TGTTCCTGATTCTATTCGGTGCGATAAAGGCGATCGTATTCGATTCAAGT
CTGATGTTCTCACTTTTAATCAAGTAATTCGCTCTTTTCTTTGTTTCATG
TTGTTTGATGATTGTTTTGTGCTATTTTTAATTGGAATTTAGTGAAAGTT
GCCTGCTTTCGGGGTTTTGTTGGTGTGTACTGTGTACTTTAGGATTTAAG
ATTATGTAGTTGTAGTACGTTTGAAATGATTGCGTGTTGCGTGTTTGATC
TCTGAATTCAATTGAAATATTTTGGAATTAAGTAAGTATATGTTGAGTCA
ATTCTAATTTGAGCTTGCTGCAAATGGTGGAAGTGATGAATTATGAGCTG
TAGAGCTCAGCAATGAGGTAGTGTGGTGAATTATGATGATGATGATGCTC
ACCATTTGCGATGGTTGCGTATAGTCTCGTGGAACTAGTATGAGTATGTA
AAGCTTCTTTTGAAAAATACTGTGTTAGTTTACACTTGATGTTGAACTTC
TTTTAAGGAATGTACAACAATCTATGACAACTTTTCGCTTTCCAAATTTA
ATATCGAGGATGGCGTTTACTAAGACACGTAACTGTGTATGTCTTTTTCT
GCCTGATATACTAATGTTATATTAAAAGACGGCTGCTTTTTGATGAACCA
CTTAGAAGTGAGAATCCTCTTATGCTATTGACTTTATTGTGCGGCCGACT
AGTTGGGAGGATCACTTGACAAAGTTTCATTGGGTCCTCAAACTGCTAGG
ATGTATAGTATGTATATGTTTACACACTTGCATCCAGTGACATGAATGTG
TGGTTACGTGTGAGCTCCTCTTATGCCCGATTGCTGTCCTGGTATGTAAT
ATAGCTGAAGTTATCTGTCGGCTAGCACAATTAATAGTAAATGAAAATTT
TTGTTTGACTATTCAGACTCTTAGTAATAACATACAGTTGAACTATACCT
GTATTAATTTTTTACTAGAAGCAAGAATCTATCTATTTAAAAAAAATACC
ATTTTTACTAGACAAAATTAGGGCTTCATCGACTCTGTTTTTTTGTGAAA
AATCTCTGAATACACTTTTGATAACCAATACTTTCCAGCTCTTCAGCATA
ATAGAATCCTAGGGTGATGAATCTCTCAGTTTTGCATCTGAACTAGTCTT
GTGAAGATTCGTTTGCTAGCTAAAACTTAGAAGGGTCTAATAACCATAGC
TTTCCTGTGACACCGGGGAAGTTCCGTTGCTATAAATAAGGGAACAATTT
AACCTGATAGATTTGCATTTTATGTTTACAAACAATGGGTGAGTTCTTCC
AGAACAAATGGTGCAAGGGCTGCTATCAAGTATGCACGTCATTCCCCATA
ACTAGCTTTATATGACATCTATCTTAATATGATATTATTGTTATTCTTGT
GGTTGTCATCTGTTACCAGAGAAATATGTTCCATCTTGCAACCTAAATTC
ATTTTGTTTTCTTTGCACTGGTTCGTTTGCTACAGATGTCAGAGTTACTG
AATCAGAAATCTTCAGTACAAGGAAAAGTACCTTCAGGATACTTCAATGC
TATGTTTGATTTAAGTGGTTCTTGGTTAAACGACGCTGCAGAAGCAGATC
ATCTTGCTTTTGATGGGTACTTTATCTCTTTGTACTATCTACACCTGATA
GCATCTCCACTAGTACTGCATGACAAGGTTAAGAAGTCTGTTCCTTCCCA
CTGGAATCCTGCGTCCTTATCAAGGTAATTTTGGTCATTGTGTTTCGTAC
ATTATTAATACCTCATTTATAAATTATAATTGAAGTTAGTCGAATGATGT
TTAAATTAAAATGCATTGTTTTCTGAGTGTCATTGAGGGTAGTTATAAAA
GTTTTAGACTAGATTTAGCAAGGGTCATAACGAATTTCCAACGCCTTGGC
ATTCTGAGCGTGTAACAAATTAGCATTCTGAGCCTTGTAGTGATTTGGGT
ACATTGGTTCAGTTTTCTTTTCCGTTTGCTTCAGGTTCATCCGAACTTAT
GGAACTCACATAATTGTGGGGTTGGCTGTTGGTGGTCAAGATATAATTTG
CATTAAACAGAGACCGTCCTCTGTAATTCCTCCTGCTGACCTGCGAGGTT
ATTTGGAGGATCTTGGGGATCATTTCTTTTCAGATGGGAGGAGTCCTCTA
CTAGAGAGGAAGACGAGAGATGGAAAACAGAAGGTTTATTGTGTGTTCTA
GTGTCTTTCTTATGTCCCTTCAATGTGATGCTTTTAAGTGGATATTTCAA
ATTGTGTAGGTTCCCGAGGTTTTTAATCGTATGCTACAGCAGCATACAAT
GCAATTCACCAGCATCACAGAAACATCAAGCAAAGATGTAAGCTCTAAAC
ACCTTATGCTTTCTGATAAACTAAAATGTGGGCCATGAATATATGAAGTA
ATTTGGGACAGGGCCTCACAATTATTTCATCAAAAAGAGGAGGGGATGTA
TTTTCACAAAGCCATTCCAATTGGCTTCAGACAGTGGCTTCCCACCCTGA
AGCAATTTCTTTCAAACTTGTACCTATTACTTCTCTCCTCTCCGGTGTTC
CAGGAAGCGGCTATCTTAGTCATGCTATCAACTTATATCTACGCTGTAAG
TATGCGATCTTGTCTCATTTATTTAATTTTTCATATGATTTATTTATTGT
TACCATTTTGTCATACATAAAGGGTTTGAATCAGATGAAATTGGTCTTCA
TGTTTGAAAAACAGGAACCTCTAAGGTTTGATTTATAGATACCGAATGTT
CAGCATAACTTTGTATATAAGATATAAATTCTATTAAGTGACAATGATCC
ATGTGCGGATCTCTCTTTCAGAATATATGCATCAAGTATCATATTACAGA
ACCAAAATGTTCTATAATTCTATCCTCTGATAACAGTCCATATTGAACAC
TTAAAGTTGTACACACATAAAAATAAAGGTTCAGCACATTATCGTGTTGA
ACTTTCGTTATAATTATCATGTTGTAGCATATGGTTCTCATTTTGTTGTT
CTTACATGAACCAGATCCCATAAATATGTAAATGGGGGATCTGTTGATAG
AAGTTAAGACGCTTCTACATGTGTCAGAAATTATTGTCAATCCCTAACAG
TATGTAAATGCTTTATCGTCGTTTTAATCCTTTTTGTTTGTTTTATGTTC
CTATATTGTACTTCATGCCTGTGGCCCTTAATGCGATAGCTTTTGTATCA
AATTAGCACTTGGGGCCTGTCTATATTTTTCTTAGCTTGGTATTCAAGAA
TATAGATAGGGTTCTGCTTATTTGTTAGGCATGTATTGGAGGAAGCTTTA
GCACCTCGTACATTATCAGTTTCATTTACTTATATGATATTGTATTAGTT
GATGATAGTAAGTACAACTTATTCTTCAGATAAGCCTGCTCTGGAGGATT
TACATTGTTTCTTGGAGTTCCAAGTCCCCAGACAATGGGCCCCCTTGTTT
TGTGAACTGCCTCTTAGGCATCAAAGGAAAAAGTCTTCTTGCCCTTCACT
GCAATTTGCTTTCTTTGGTCCCAAGATTAGCGTGAGCTCCACCCAGGTAA
TGTATTAGTCCATGCACAATTTTATTATTATTATTATTTGGGGAAGGTCA
TCTCTGTGAGAGTTGATATATATATATAGAGTTTTACTCCAATAGAAACC
TTCTTAGTCTAGAAACTAAAAACCAAGTTGAAATATCACTAAATCCTAAA
GCAAATACCACTAAATTCTTAAACAACCTCATCTCCACCTCCATCTTCAC
CAACCCCACCTCCATCTTCACCAACCCCACCTCCACATCCGCCACTGCCA
CCACCTCCGTCTCACCTCCTCCATAACCACCACCACCTCTATGCCGCCCG
CCTCCTCCATCTCCACCTCCATTATTTCTCTAACAACACAATCTCCACCT
CCATCTTCACCAACCCCATCTTGGTCGCTGCTTCAACCTTTTATCTTCAC
CAACCCCATCTTGGTCGCTGCTTCAACCTTTTTCAGCCCTGTTCATACTT
CTTTCTCCACCTCGGCTCAACTTCAAAACGCCGCGGAGCCGCCACTATTC
CGGCAACGCTCTGATATATATATATATTCTGCCTTTTGTCTAGGCATTTT
GGGGAGGTATCTTGTACTATATCATTATTACTAGTTCTTACTGTAGAGTA
CTCAGATTTAGAGATCATCTAGAACTTAGTTTTGAGGTTAATAACATGGT
CTGCTTCAACTATGTTTAAAGTTGTAGATGTTATTGGCAAGCCTGTGCCT
TCTGGAATCTGTTTACAAAGTTTAGCTGATCCTATTGGCCAAAAATTGGT
TTTCAATATTGTGAATTCTGAAGGATTGTATTTTTTTTTTTAATTCAAGT
GGTGGAGCATTTTATATATGATCAGCATGATATTGAATGTGGCAAATGAT
ATGAATTAATTTTGTTTCAAACATAGTATTGCAGTTGGCTCATGAAATAC
TTGGTCAATATTGTGAACACTCGCTTGTGAAGTGATACACATGTTTGTAT
TAATTATAACTGTTATCATTAGTTTACTGTCTTTTAAGTAACTTGCGCAT
TTTTTTGTGGTTCAGTTTCATGAACAGTCCTAGGTTACAGGTTCAATTAA
TGTAGATACCTCCTATCTTTACTTTTACCATGTTGATGGAAAATCTTTTT
TATTTGATATAAGAAAGAGGTGAAGTGAGGTTATATGTTCTGCTCTTATT
AAGTCGTGGTTCGTAGCTAGGTGCTATATCCATCCACTATTTCTTTTTGC
AAATTTTCCTTGCATCTGAAACACTGTGGTTTACTTTAGTTTTTGACCGA
TGATAAGTCGAAATAAATTGCGCTGACATTATGAATTAACTTTATAAATG
TTAGCGATGAAGTAAGTGCCATTCCAATATATTAGAAGATTGTTGCTTTT
TGTGGTATGTGTTGGACACTTTAAATATTTCATATTGTTAATTTATCAGG
TTGGTAGTGGTAAAAAACCAGTGGTTGGCCTCCGTTTGTTCCTAGAAGGT
AAGAAATGCAACCAGTTGGCAATACATGTGCAGCATCTTTCTAGCCTTCC
AAACATGATGGAGCTTGCTTCAGTTAACTCTTCTGTAGCATGTCAATGGC
GTGGGTCAGATGATTATGAATCAAATGAGCAATTCTTGGAACCAGTGAGA
TGGAAAAAATTTTCAAATGTGTGCTCATCAGTGGTTAGGCATGATCCCAA
CTGGCTGCAAGGCCAAGAATCAGGTGGTGCATTTGTTGTGACTGGTGCTC
AGCTTGTCAGCAAGGGGCAATGGCCAAAGACAATACTTCATCTCCGTTTG
CTCTTCACTTACCTACCCAACTGTACTATTAGGAAGACCGAGTGGGCAGC
TGCACAACAATCTTCTCGAAAGTCAGGTTTCCTGACAAATATAAGTACAA
CCTTCTCATTTACCCAGAGAGCTGTGACTGATGCACCAAAGCAGCTGCCG
GCTGCACTGAATTCTGGAGTATACCCTGAAGGACCACCTGTGCCGCTTCG
TTCTAAGAAACTGCTTAGATACGTAGATGTGAATGAGGTTGTGCGGGGTC
CACATGACACTCCAGGTCATTGGTTAGTTACTGCTGCTAAGCTGGTTTCT
GATGGTGGTAAAATTGGCATGCATGTGAAGTTTGCATTATTAGATTATAC
ACCGGCATAGTGAGCTTTTTGTCGCGGGATATGAAGTGGACTGCTGGGTA
GATCATACTGATGTGTTTCGTTTTCTGGAATATATGAGGAACATCAGTAT
ATAGCGAGATATATTTCTTAGTGTACAGAAAGATGAGAGCGGGAGTGGCG
ACATGGGGATTATGAACCTTTCCAGAGGTTATCGTTTGGTAATGATTTAT
GTCTTTTTCAATGATTTATAAGAGTATATATATTGTAGAGGAAATATTAA
CCAGTTCTTGTGAATGGATTTAGTTGCAAGAAAAGATCTGTTCCCTATCT
CAAA