XM_017379520.1 | CarrotOmics

Resource Type:

mRNA

Name:

XM_017379520.1

Identifier:

XM_017379520.1

Organism:

Daucus carota subspecies sativus

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.

Transcript Id:

XM_017379520.1

Product:

protein LHY, transcript variant X8

Sequence:

AAAATATTCGAGAAACAGTCTCACAAATTATAGTGGCTGAGAAATGAGCA
CTCCTTTTCTTCCACCTATGTCTTCATCTTCTTCTTCCTTCTCTTCACTC
TTATTAAAATCATTCTATCTCTAGTCCTTCGATTTTTCGGATCACATATC
ACTACCAGATCCACCAACTCTCTGTCCACGTAGGTTTTGGTGATTCGAAG
ACTACGGGGATATGATGGATGAATTCTGGAATAGCTAGTTCGAACCAGAT
GGATTTCTGTAAATGAGAGAAGGCTACTACTTTCGGTTTCGGATTGCTTT
TTTCGCCCTCGTTGTCGCCCTACATGGACCCTAATTACTCTTCCGGAGAA
GAACACCTCTTGCATACTAAGACAAGGAAGCCTTACACAATTACCAAGCA
ACGCGAGCGATGGACTGAGGATGAACACAATAGGTTTCTCGAAGCTTTAA
AGCTTTATGGTCGTGCCTGGCAGCGTATAGAAGAACATATAGGAACCAAG
ACTGCGGTGCAGATCAGAAGTCATGCACAGAAATTCTTTACAAAGCTGGA
GAAGGAGGCTCTTGTTAGAGGACCTTCGACTGGACAGGCTATTGACATTG
AAATACCTCCTCCACGTCCTAAAAGAAAACCAAGCAATCCTTACCCTCGA
AAAACCAGTGTTGGATCTTTGAGCTTACAAGCTGGAACAAAAGATGGGAA
CCATTTGATATCAGATTTTTCTCAATCTTCTGCTGCACATGTACTGGACT
TGGAAAAAAAACAAACTCTTGAGAAACAAAGTGCTAATCAGCAGCTTGAA
ATCGTAAAGAAAAATCAAAACGGAGTTGATTGTGCTGAAGCATTTTCTTT
CTCCCAGGAAGCTCTTTCTGGCCCTTTGTGTTCAGAAAATAAAAGTACCG
TTTCAAAGACAACATCGACTAATCATTGCAATTTTAAGGAGTTTGTTCCC
AATTTTAAAGAGGTAGTTAACCAAGATGCATCACATGAATCTTATCTTAC
CCTTAAAGCGAGTGGTGGCCGAAATGACAAAGAACATGATACCAAGCAGT
TGGTTGGAGATCTTCCCCCTTCTGAGACTGCGAAATTAGGAAACTATCAT
CCTACACATGATAAATTGTTGCAAACACAAAAAGTAAATGAACTGAAGCC
TCCTGTGAATTATGGTATCTTGTCATCATATGATATGCAAGCTGCTGCAC
ATTACCCTAGACATGTACCTGTGCACATTGTGAATGGAAGCCTTGAAATT
GCTCAAACTGGTGCCAGTTTATATGGCAACGTAGCCCCGGCCTTAACAAC
TGAACATGAGAATAATGCTTCACGATCTTCAGTTCATCATTTTCCTCCAT
TCCATTCTCCTTTTACCCCAGTACAAAATCCTCAAAGTGATTGTCACTCA
TTGCTCCCGATCCCCGCTACTTTTACTAGTCTGGTCGCATCTGCTCTACT
AGAAAACCCAGCTGCCCATGCTGCAGCAAGCTTTGCAGCTAGATTTTGGC
CTGTTGCTAATGTTGACCCTTCTGCAGATCCTCACGTGGGCAAGATGGAG
AATACAGGGCCTAGTATGGAAGCCCTTGCTGCTGCTACTGTGTCAGCCGC
TACTGCTTGGTGGGCATCCCAAGGCCTACTTCCATTGTGCACTTCCTTTA
ACGCTACCTGCAGTGCTGCCCCCACAATTACAACAACAATGGAGAATAAT
GAAGCTAGAGTAAGCAATGATAAAAGCGGAGAAAACCCAGCTGATCTTTC
CTTGAAGGATCAACAGCTAGAGCCAAAGTGTTCTGAAACTTTGCTAGATC
ATCAAACAGCTGTAAAGTCTCCACCTCTGTCATCATCTGAGTCTGCAGAA
GGTGAAAGTGAAAAGCTGAATATTAAGTTGAGTAATGTTGACCCTGAGCA
AGCTGAGGCAGTCACCAAAGCTCAAGATTTAAGCAAAACGAAGGATCAAA
AGCTGGTGGACCGATCTTCATGTGGCTCTAATACTGCCTCTAGTAGTGAA
GTAGAGACAGATGCTTTGGAGAAGCATGACAAGGAAGAAGCAAATGAACC
TGATTTAAGTCTCCAAATTAGTGACTCTACTAATCGTCGTGGTAGGATTT
GTAGCAATCTGAATGAATCCTGGAAGGAAGTCTCGGAAGGGGGGCGACTG
GCCTTTCAAGCATTATTCTCTCGAGAAGTATTGCCACAAAGCTTTGCATC
TCCTTATTGTCATCAAAAGTACAGTATTGGGGAGGATAAACAACACTTAT
ACAAGGAAGAAAATGAAAGATTACAAATTGATATCAACAGCAAAGCATGT
GGGAGTAATGAATTTGTGGAGCATAATGTTTCCTTGACAGGTGGAAGCAA
TGAGGGAGAGGGAACTCTGAGCACGGGACTTGGATGTTTGAAGTTCAAAG
CCCGCCGAACAGGGTTTAAACCTTACAAACGGTGTTCAGTGGAGGCCAAG
GAAAGTAGGGTAGCAGCAGCATCTACCATCAATCTAGAAGAAGGTAAAGC
TCCTAAAAAAATGCGATTGGAAGGAGGTGCTTCCCTTTAGTAGTTGGCTA
CACAAGCATTTAATGATTTTAAGAGACTTTGTCATAATGGTTTAAATATC
ATAGTTATATTACTCATGAGACTCTGTTGTGTAGGTATCTTCTAAATATT
TTTAAATGTATATTACGTGCTCTCTTCGGAAAAGCACCTGGAGACTTTTG
AGAAAATCTAAGAACTTGTAAAGGAAATGAAGTGTTCCTTTGTTGTGGTT
A

Sequence Length:

2751

Sequence Checksum:

4b7c0faa046b5bb0a2674eab70a30d26

View location in JBrowse:

DCARv2_Chr2:30639744..30645570+

Protein Sequence:

MDPNYSSGEEHLLHTKTRKPYTITKQRERWTEDEHNRFLEALKLYGRAWQ
RIEEHIGTKTAVQIRSHAQKFFTKLEKEALVRGPSTGQAIDIEIPPPRPK
RKPSNPYPRKTSVGSLSLQAGTKDGNHLISDFSQSSAAHVLDLEKKQTLE
KQSANQQLEIVKKNQNGVDCAEAFSFSQEALSGPLCSENKSTVSKTTSTN
HCNFKEFVPNFKEVVNQDASHESYLTLKASGGRNDKEHDTKQLVGDLPPS
ETAKLGNYHPTHDKLLQTQKVNELKPPVNYGILSSYDMQAAAHYPRHVPV
HIVNGSLEIAQTGASLYGNVAPALTTEHENNASRSSVHHFPPFHSPFTPV
QNPQSDCHSLLPIPATFTSLVASALLENPAAHAAASFAARFWPVANVDPS
ADPHVGKMENTGPSMEALAAATVSAATAWWASQGLLPLCTSFNATCSAAP
TITTTMENNEARVSNDKSGENPADLSLKDQQLEPKCSETLLDHQTAVKSP
PLSSSESAEGESEKLNIKLSNVDPEQAEAVTKAQDLSKTKDQKLVDRSSC
GSNTASSSEVETDALEKHDKEEANEPDLSLQISDSTNRRGRICSNLNESW
KEVSEGGRLAFQALFSREVLPQSFASPYCHQKYSIGEDKQHLYKEENERL
QIDINSKACGSNEFVEHNVSLTGGSNEGEGTLSTGLGCLKFKARRTGFKP
YKRCSVEAKESRVAAASTINLEEGKAPKKMRLEGGASL

Relationship:

There are 2 relationships.
Relationships
The mRNA, XM_017379520.1, is a part of gene, LOC108208909.
The polypeptide, XM_017379520.1, derives from mRNA, XM_017379520.1.

Cross Reference:


NCBI Gene	108208909
NCBI Nuccore	XM_017379520.1

Gene:

LOC108208909

Model Evidence:

Supporting evidence includes similarity to: 10 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 25 samples with support for all annotated introns

Gbkey:

mRNA