LOC108221735 | CarrotOmics

Resource Type:

Gene

Organism:

Daucus carota subspecies sativus

Name:

LOC108221735

Identifier:

LOC108221735

Cross Reference:


NCBI Gene	108221735

Relationship:

There are 2 relationships.
Relationships
The mRNA, XM_017395592.1, is a part of gene, LOC108221735.
The genetic_marker, MK004091 K1535, is adjacent to gene, LOC108221735.

Analysis:


Name	Description
Carrot Genome Assembly DCARv2	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 Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below. These sequences can be viewed in JBrowse here. 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
NCBI Daucus carota subsp. sativus Annotation Release 100	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.

Transcripts:


Transcript Name	Identifier	Type	Location
XM_017395592.1	XM_017395592.1	mRNA	DCARv2_Chr5:33786443..33800884

Sequence:

CTCGGAAGTTGTCAATTTTGTTGCTTTTTCTAATCATTTTTAGGGTTTCT
AGAGTTTAATATCTGATTATGAAACTGTGTTGAGTATCTGCAATTTTTAA
TGTATAGGCAATCATGAGCAACGAGGGAGAAAAGACTTGCCCTCTCTGTG
CTGAAGAGATGGATTTGACTGATCAGCAGTTGAAGCCGTGCAAGTGTGGT
TATGAGGTCAGAAATCTTATTTACATGTCTCTTTGTTAAAATTTTGCAGC
AAAATACTTAGTCTGATTAGCTTTTGGTAGGATAATATTCATTTTTATTT
GATTCTGTACTCTTATGGAGAGTAATTATAATATGCTAAATCAGTGTCAG
ATATTATGGCTGATGTTTTTGCATTATGTGGAAATGTTTTTCCATTTTAA
AATTTTTATTATATTGAAAGCTCTTGAAATTGTTTTTATCTATATTATTT
GCCAACTGCCATCGGATTTTGAATTAATAAAACATCTCTACCCAGCATCA
AGTTATTTTAATCTATAATTTTTTAGGTCATTGGGAATCTGTCTTTGTGA
AACAGACAAAAAGCAGCAGGGATTGTTGCTAAGTTGTACATTTTTGTTTG
GTTTATTGGGGAACATTGTGCATTTCTTCAAGTTTCTGCGGAGGACATAT
ATTGAAATTAGTGTTAAGTGTTTATGTTTCAATATATATTTGTGTTGCAT
ACTCACAGTGGAAACACTTGTTAGGGTTAGTAAAGAATCTAATGGGACAT
TGCTCTAAATACAGTTTATCAAAATTTTAGCTAAGTGGCTGATTTGTGAC
AGTGATACAACTTCCATAATTCTTTTTTTTTATTATTACCCATATCAGAT
GTCATAGGCTGATTGTTGAAAGCACTAAAATGATATTAAAAAAACGTCTA
ACAGAAGTAATGGAAAGTTTAAAGTACAATCGGTAGATATGCTACAATTA
AGCTTTTTGCATAGATTAAACCAGCAGTAGTGACCGTGAAATTTATACTC
TTTGGTGTGAGTTTTCATGGATGTTGACTCTCAAACCCAATAGCGTGTTT
GCTTCTCCTGTAGATTTGTGTTTGGTGCTGGCATCACATAATAAACATGG
CTGAGAAAGACAATGTAGAAGGCAGGTGTCCAGCATGTCGCACCCCTTAT
AACAAGGAAAAAATTGTGGAAAAGGCAGCTCAATGTGAAAGGTTTTCATC
TATGCATAGCTTATGTTGACGTCTGCAGATATTTTATTGACATAGTTATG
ATGACACAGAATATTTCTCGTTGATAGGTTGTTGTCTGAGTTGAATGTGG
AGAAGAAAGGGAAGTCAAAGTCGAAAAGTAAAGCACCTGATGGTAGAAAG
AACCTAAGTAGTGTTCGAGTGATTCAACGAAATCTTGTCTACATTGTGGG
GTTACCTCTTACTTTGGCAGATGAAGACGTGTGTATATCTCCTCTTTTTC
TTGCTTCTTTTTGTCTATACTTTTCCGCTCGTTTTTTTATCACCTGTATA
TATATTGTTTTATGCAGCTCCTACAAGGAGCGGAATACTTTGCTCAATAT
GGGAAGGTGCTTAAAGTGTCAATCTCTCGTACGGCAGCTGGGACCATTCA
ACAATTTCCAAATAGCACTTGTAGTGTGTAAGTGTTTCTTTTTCTGATTG
AAATGACTTTAAGATTGCAAGCATAATTAGGCCTACATATAGAAATATTT
TTTTGTATAATTGTGTGTCTAATAGATTGCCTGAATATTAAGTCGGATTC
CTTATTCTTGTAAAAATTTGAAGCCAAGCAGCAGGTTTTCAGGTCTTAAT
TTGGGCAATGACCATCTTGAATATGTGCGTTTAGGTTCTTATAATTGTCT
GATGTTAATAAAGTTATTAAAAGTCATATATGAGATGTATATTAACTCTT
AGATTATCAACCTTTGTTTTTACAGATATATTACTTATTCAAAGGAGGAA
GAAGCAGTTCGTTGCATTCAGTCAGTGCATGGTTACACATTGGAGGGTAG
ACCATTAAGGTCTGATTCTGTTGGCTTTTGTGGATTGCAGCAGTAATTGT
TATCTGTTTGCTTATTTACTATTCTTGTGTTGCAGGGCCTGCTTTGGAAC
CACAAAATATTGCCATGCATGGCTGAGGAGTGTGGTATGGTCCCCAATTT
AATTAATACTTAAATTTGACATTTTGAGTTTGTGATTTTGTGCTGTTCTG
ATCATCAAACTTTGGTCCAGCCATGCATCAATCCTGATTGTCTATACTTG
CATGAAATTGGTACACAAGAAGATAGTTTCACTAAAGATGAAATAATATC
AGCATACACAAGGTATTGTATAATTGTCATGTGCATTCAATGTATTGTTT
TATCAATCATATCTTTTGGAAGAAATCAATCTCCATCTAGCCAATATGCA
AATTTGATTGCTTTTCTGAATGATTGTATACTTACAATAATAAATTAGTA
TCTGCACTTCCTCCATCAGACGTGAGCAAACTATAAATTCAGCATTCGGT
ATAATATAGAGGCGCTCAAACAGCTTTGATAATTTGTTTTTATCATCACA
AATACAAGATAATACATTCTATAAATTGTCTTTTTGCAGCTAATGTATAC
ATGTTTATAGAGTTGAAATATTGGATATGTGGTTGACAAAACTTAGATTG
CTTGAAAATTGTTTTTATCAGTTATGCTTTTCTGTGCTGGATTAGTGGGA
ACCCTCTGTTTTGATATGTATACTGACTTCAAAGCATAATACTTTGCCAT
TGCATAATATAGTAGTGCAACGTAAACAATATCTACTGTCAAATGGTTAC
ATTCAACAATATAGTGGTGTTACTTGCACAATATGACAATTGAATGATAA
CTTCTAATGCTTAAATGTTTATAAATGAATGAAGACCTGAAATTACCACA
AAGTTTGACTTAGAAATTGCCTATTACTTCAGCAAGGGTGTTTGGTTTAA
TTTTGAAGTTTTTATTTGGTTTTTTCCCATATTACACTTTCACTCGGTAC
ATATTTGTGGCATGTTTTATTGAGTAGGCTTGCCTGATCGATCATCATTT
GATACAATCAACTATCTATTTTCTGCCTAATTAACTTGCAATGTTATTTT
GAAGAAATAGAGTTGAACTGAGTGTGGGTGCCACAATCGACACGCAACGT
CGATCTGGGAGTGTATTACCACCACCAGCAGACGACTTCTGTAATGACAG
CTGCTCCTCATCTGGAATACATCATAATAAAAGCTCAACGGATGTATGTT
TTTGAGTACAAATTATTTGTATTTGGGTCTTCTTCCTTTTAACATAAATC
AGTGGATTGCTCAATCTCGTGTGTTTTTAAGCGTTGGTGTACAAGTATGC
TATAGAGTAGCAATTCTAAAGGATACTGAATTACATACGTAATTTTTCAA
ATAATATAATTAGTAATCGAGGTTTAACTCTATTAGCCACCAACTGATAT
ATATAGACTGTGACCACGACACGTCTTTTTTTATTTTTGATATGGTGCAG
AACCTTGACATCTCTTCTCAAAACATATTGGAGTCATCTGTCTGGCAAAC
TCCGGCAAGCAGTGTGAGGGGCTCTCCACCAAATAGTCNNNNNNNNNNNN
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NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNATTTATTATAGAATTTAATATATACAAGT
TTAAATTCTTCTCAGGGGAGCGCGTGCTTCAAATAGTCAACCATCACCAA
CAAGCATGGCAAGCTCAAATGGACCTTCTAAGCAGAAATCTGATACAGGT
GGCATTTCAGTCGCATTTTCAACTGCAGTAGTGAGCCCAGCCAAAGTCTC
CTTAATGCACAATACTTCAGGAAAGAAACTTAATGGAGAAGGTTGGTTTC
CCTTACAGAGGAATAAATCTGTTCCAGTAGCATCTGTGGGAATACAGGAT
GTAGATAAGCAACAAAAGTCATCGAATACTTCCACCAAGATTGGACATTT
TGATAAACTAGTGACAAGTGACCAGATATCTACGCCATCGCCAAAAGTAG
ATGGGTCCACAAGCATGCCAGATATCACAGTGCAGTCTTGCGGTATTAAT
TCAGAAAGAAATTCACATCTACCTGTAGAGAGTAAATTTAAGGAATTATG
TTCTGATATGTTGTCTTTAAATATAATTACTCATGGGCCACAGCACGTAG
ACACAAAATACAGAGAACTCTTGTCAACAGATGCTGCAGCAAAGGATGCA
TCCTCCAGTAAGGATCCTGTTGCAGCAAGGGATCTGTCTGAATTTAAATT
AGTGTCGCCGTCGCAAGTAGCAGAAAGTGATACTTGTAAAGTTAAGGATG
ATATACAATCTTTTAATATACAAAGACGCAGGGATCCTGAAGTTACCAAT
AGCACAGATAGTAGTATAGGTCAGTTATCAGATAGTTCTAGGGATCTACA
TTCTCAAGAGTCTTTCCATATACCCAGCACCAATTTTGATCTAAATAATG
TAGATAATCAACCTAGCAAGTTTTCTGTTCCGCAAGCATATAATGCCCCA
GTTATTTCGAATGGTTATGCTGGGAACCAGACTAGAAGTTTTGATTTGGA
TACCAGTGCTAATGATTCTTCTTATATGCTACAAGATGAACTGAAATTGC
ATGATGGAAGACATGGCAGTGCGTTAGTAAACCACGATAGTATTTTAGCA
GACGGAATGGGAGAGAGCAGCATCATATCAAATATTTTGTCAATGGACTT
CGATTCATGGGATGAATCTTTGGCTTCACCGCAGAATTTGGTTAAGTTAC
TAGGTGAAACTGATAAACAGCTGGGTTCTCTTGGTGCATCGAATACGAAG
AAAGTACAAAACAGCAATCAGTCTAGGTTCTCTTTTGCAAGAGAGGAACA
TCAAGCATCCAATTTTGGGCCATCATCTGCTGGCGTTGAGCAAACTCTTA
GGAATCATTCTTTTACAAATGGTTTCAAGGACAATGGAAACCATTATCGC
AGTGGTACTGCCAATGGTTATTCTACTTTGAGTGCGCATCAACCTGGTGA
TTTTGCAAGCACCCATTTTCATAATTCACCGAACAGGTTTTCTGGTGAGT
TCAGAGTTGCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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NNNNNNNNNNNNATTTATTATAGAATTTAATATATACAAGTTTAAATTCT
TCTCAGGGGAGCGCGTGCTTCAAATAGTCAACCATCACCAACAAGCATGG
CAAGCTCAAATGGACCTTCTAAGCAGAAATCTGATACAGGTGGCATTTCA
GTCGCATTTTCAACTGCAGTAGTGAGCCCAGCCAAAGTCTCCTTAATGCA
CAATACTTCAGGAAAGAAACTTAATGGAGAAGGTTGGTTTCCCTTACAGA
GGAATAAATCTGTTCCAGTAGCATCTGTGGGAATACAGGATGTAGATAAG
CAACAAAAGTCATCGAATACTTCCACCAAGATTGGACATTTTGATAAACT
AGTGACAAGTGACCAGATATCTACGCCATCGCCAAAAGTAGATGGGTCCA
CAAGCATGCCAGATATCACAGTGCAGTCTTGCGGTATTAATTCAGAAAGA
AATTCACATCTACCTGTAGAGAGTAAATTTAAGGAATTATGTTCTGATAT
GTTGTCTTTAAATATAATTACTCATGGGCCACAGCACGTAGACACAAAAT
ACAGAGAACTCTTGTCAACAGATGCTGCAGCAAAGGATGCATCCTCCAGT
AAGGATCCTGTTGCAGCAAGGGATCTGTCTGAATTTAAATTAGTGTCGCC
GTCGCAAGTAGCAGAAAGTGATACTTGTAAAGTTAAGGATGATATACAAT
CTTTTAATATACAAAGACGCAGGGATCCTGAAGTTACCAATAGCACAGAT
AGTAGTATAGGTCAGTTATCAGATAGTTCTAGGGATCTACATTCTCAAGA
GTCTTTCCATATACCCAGCACCAATTTTGATCTAAATAATGTAGATAATC
AACCTAGCAAGTTTTCTGTTCCGCAAGCATATAATGCCCCAGTTATTTCG
AATGGTTATGCTGGGAACCAGACTAGAAGTTTTGATTTGGATACCAGTGC
TAATGATTCTTCTTATATGCTACAAGATGAACTGAAATTGCATGATGGAA
GACATGGCAGCGCGTTAGTAAACCACGATAGTATTTTAGCAGACGGAATG
GGAGAGAGCAGCATCATATCAAATATTTTGTCAATGGACTTCGATTCATG
GGATGAATCTTTGGCTTCACCGCAGAATTTGGTTAAGTTACTAGGTGAAA
CTGATAAACAGCTGGGTTCTCTTGGTGCATCGAATACGAAGAAAGTACAA
AACAGCAATCAGTCTAGGTTCTCTTTTGCAAGAGAGGAACATCAAGCATC
CAATTTTGGGCCATCATCTGCTGGCGTTGAGCAAACTCTTAGGAATCATT
CTTTTACAAATGGTTTCAAGGACAATGGAAACCATTATCGCAGTGGTACT
GCCAATGGTTATTCTACTTTGAGTGCGCATCAACCTGGTGATTTTGCAAG
CACCCATTTTCATAATTCACCGAACAGGTTTTCTGGTGAGTTCAGAGTTG
CAGGGTTTTTTTTACAGATAGTGTCTATTGATATATATTTTATTATTTTG
TGCAAGTGTGGCATTTTATTGATAGATTGCTTGTGGAGAATAAATACTAA
ATTTGTTGTTAAATATGCTCATCATTTATGCCTTTAGTTTTGTTTTCTTT
TACTCCGTATGTGCATTCATGTACATTAAAACTTTTGGCGATTTACTCTT
TAGCTAGTTCTGTAATCGACTTAGTTGTGTGAGAACTGACATGGGTTTTG
TGCTTTTGGCTGAAAATTGAGCAAATCATTGTTCTTGGATCTGCTGTGAC
ATGCTTTTGTTGATATTCTCCTTCTGCTTTTAAAAATTGTGACTGAGATG
CTTTTTTTTCCTAATTTTTTTCTGATATGATTTATTGTACTTTGATGTCA
AAATAGTTTCTAGAGCACCTGTAACAGCCCCTCCTGGATTTTCCGGGCCT
ACCAGAGCTCCACCTCCAGGCTTTTCCTCTTTTGAAAGGATGGAACAGAC
ATTTGACGTAAACTCTGGTTTGTATTTTACACTTCACATTGAATGATTTG
TTTCAAGCACATCTCACATCTCTGAACTTACATTTTATTGCCTGATTTCT
TGTAGGGAATCATTTGCTCAACAATTCATCTTACTTGAGAAATGCTAGTC
AGTCACCTTCTAGTATGTATAATGATTCCACCAATGCAGATATAGAGTTT
ATTGACCCTGCAATATTGGCAGTAGGTAAAGGCAGACTTCCTAATGGGTT
TAATAACCCTAGTTTAGACATGAGGTCAACTTATCCTACCCAGATGAGTA
ATTATGAGAATGAGGCAAGATTGCAGCTAATGATGCAAAGATCTGTTTCA
CCACAGCAGAACCCCAGATATGTCGAAATGGGTAACAGTTTTTCTTCTTA
TCCGGATAATTATGGAATGCCTCCAACGATTTTTGAGCAGGCTTTGGCAA
ACAATGGATCCCAGTATTCTCAATTTGGTCTTTCACAGTCCAGAAATCAA
CTTGTGTCGAGCGGTAGTTGGGATGGTTGGAAAGAGGTTCTGAGTGGAAA
TGGCTCAAATGCGGCAGAGTTTCTTAGATCGGAGAGATTGGGAGGAAATA
AGTACTTTAGTGGTCGCCAGGATTCGAAGTACCGGATTTCCAGTTCTGGA
GATTTATATAATCAAACATATGGGATTTGAACTTTGTCTAGTGGACTAAT
CCCTTTAATGTTGAAACTGATATAGAATGACTATATCCAACTTGTCATGA
CAGCAGTGAACTGTAAAAATGTGGCTGGATCTTGACTGGTTTTACTGGTT
AACCTGCTGATTGGCTGGATCTTGACTGGTTTTACTGATTAACCTGCTTA
TTGGTGGAGTGAACGTTCTGATAACCGTCTCCTCCAAAACCAGCAGGTAA
AGAGGAGTTTATGTTGTTACCATTAAATAGTAATACACAAGCAGAGAGTT
TAATATAATCTGAGTAGTTTTTTGGTTAGAAGCAATAAGATCTGTACCAG
TTAGGAACAAATAGTGATTATTTATACCATTATAGTTGGTACCGAAAACG
TAATTATTTCTTGAGAAATGCTATGGGCTCCAAATTGGGTCTCAAATTTT
TTTCTAAATGATGTGGCATCAGTGACATGGATTGGTGGTGTTGATGTGCC
TACATGGGGGGTCCATCTTATTTGATAGTCATATTACCAATTAAAAAATG
CCACATTTGGGATCCAATTTGGGTGCTGTAGCATTTTCTTTCTTTCATTC
CCCACAAATCTATGTGAGGATAGATGACTTTGTTCCTGCCCATTTTTTTT
GCTAAAATCATAAAAAAGTCCAGGCTATCTTTCTTTTCCTCTCGCATCTT
TTTTTCACAAAAATTTAGAATGTTAAGTGAATTCCTATCCCTTCCCATTT
ATTTCAGTGGCCATTCAGGGGAAACTTAAAAAGTTTATGAACATTCTTGT
TCCCCTGTCCTGGACTCTTGACCACGGTTTTGTATGTGAAGTAACAATAT
TGGGAAAAAATTTCGGCATTTTGGGTCCCAGTAATAATTACAGTAAAAAT
TGTTCTTTTTTAAAATTATGTTGCATCTTCCTTGTGTTTATTTACCTGCA
TTGTGCCATCTTCTGTTTTTATATACATGTATACCCTCATGCAGGAAACT
AAGCTATCAAGTCTTGGTTTGAAGCTGCATGATACAGAAAGGTACACAAG
ATCCTATTGATTATGGTTTATTATGCTAGAAGAGCCCAGGATCGAAACTG
TGAATCAGGATGAAATCGCAGGTTATGAACTTTAGTGTTTACTTTCTTGT
TGCTGGAAGTGGCTCTTAAATTATTGCTTCAGCTGTCAATTTGTGCTATA
GAAGTTTTGAGCAAATACTGTCTGCTGGAAGTAGCTCTAGTTTTGTTTAC
CTTGTTGCAAAAAGAGACAATTTGTTTACAGTAGTTTTGAGCAAATACTG
TGCAAGTTCAGTGTTTTATCATGCTACATGCTGTGAGTTCCAAGTTTCCT
TGTTTTTCTCCCAAATATAAAGGATTATTATCCCACTTAGA

Sequence Length:

14441

Sequence Checksum:

de0809820318aa93f0c7dc5291241efb

View location in JBrowse:

DCARv2_Chr5:33786444..33800884+

Gene:

LOC108221735

Gene Biotype:

protein_coding

Gbkey:

Gene