XM_017363271.1 | CarrotOmics

Resource Type:

mRNA

Name:

XM_017363271.1

Identifier:

XM_017363271.1

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_017363271.1

Product:

U-box domain-containing protein 4, transcript variant X1

Sequence:

ATGGCTACAGGTGCGATGGAGATATCAAAATTGAAGGCGCTTCTAAAAAA
TATATCAGGTTTATTTCATTTATCTTCTCGTGATAACTTAAGCTTTGAAC
CAGTTCAGAGGTATTATCAAAAGGTTGAAGAGATGTTCAAGGTGATGAAG
CTAGTGCTTGATGCTATTAATGATGCTGAAATAGCTTCTCATGAATCACT
TCAAGAGCCATTTGCAAGCTTGTATGACTCGGTTGATGAATTAAGAGAAA
TATTTGAGACGTGGCATCCATTAATGAGTAAAGTTTATTTTGTTCTGCAA
GTTGAATCCTTAATGATAAAGGTCCGTTCATCTGGGTTAGATATTTTTGA
GTTTCTAAAAAGTTCTGATCAACCTCTCCCTGTTGAATTGAGCACGGCAT
CTCTTGAGCACTGCCTCCAAAAACTTAAGCATTTGGGATTGGAACAAACA
TCAGCTGTTATCACAAAAGCTACAAGGGATCAGGTGGAGGGCTCTGGACC
CACTTCAGATTGTCTGGTAAAAATTACAGATTCTTTGAGCTTAAAGTCCA
ATCAGGAACTTCTTATAGAGGCTGTGGCCCTTGAAAAGTTAAAAGAGAAT
GCCGAGCAAGCTGAAAAAAATGTTGAAGTTGACTATCTTGATCAACTATT
AGCTCTTGTTACCTACATGCATGAGCGGCTTGTTCTGCTGAAACAGTCTG
AGAGTTATAACACTGTTCAAATACCTGCTGATTTCTGTTGCCCTCTCTCG
CTTGAGCTCATGACAGACCCTGTAATTGTGGCTTCAGGACAGACCTATGA
GCGGGCTTTCATCCGAAAATGGATTGATCTTGGGCTCACTGTTTGCCCAA
AGACGCGCCAAGTTTTGGCACATACTAATCTTATCCCTAACTACACTGTA
AAGGCACTGGTTGCCCATTGGTGTGAATCAAATGGCGTAAAGCTGCCTGA
CCCCATGAGGTCAATGAATTTAAACATACCTTCTTCTCTCCTTAGACATG
CAGCATCTGGTGCACCCCGAGATTCACAAACGGCTCCAGACTCTGCATAC
TCAAGCGGTTCGCCAGGAAATAACTTCATCTCATCTAGTGTAACCAATCG
GGAGGGAACTTCTCCATCACGTCCACGCTCATCTTCTGAGGATTCCTTGT
CTGAGGAAGCTGAAAACGGGCATGCTTTAAACATTGATAGCTTGTCCCCC
AGAAGATCTGAAAACAGGCAAGCGAATTTGGGGGATAAAAATTTGGATTC
GGGTTCCCGAACCACAATGTCACCTACTGGAGAAATGCCCAATGTTTCGA
GGACTAATGGGTCATTATCACATGGTCATAATAGGACAAGCTCAGCCTCT
AGCACACTTTCTAATGCAAACTTTTCACAAGGAATCCCTGGCGATAACAA
CGAGGCCTCCTCACTGGTCACGGCATACAGTATTGATGATTCAGGTGAGC
TTACATCAGAACGCCAGTCTGCTGCTACTTTGTCCTCTGCTCAGAGAGAG
CCTGAGTTTTCACCCCGATTTGAGACAAGATCTCGAACTCAGTCAATTTG
GCGCAGGCCTTCTGATCGATTTGTTCCTAGAATTGTGTCTTCTCCTGCTG
TTGAGACAAGGGCTATACCTACTGCTGTCGAGATCCAGATTCAGAAGATG
GTTCAGGATTTAAAGAGCACTTCGATGGAAGAACAAAGAGATGCTACAGC
TGAACTTCGTTTACTTGCAAAACATAACATGGACAATCGTATTGTAATTG
CAAACTGCGGTGGCATACCCTTGTTGGTCAATCTACTTCGATCAACAGAC
GCAACAACACAGGAAAATGCTGTCACTGCACTTCTTAATCTGTCAATCAA
TGATAACAACAAGGCTGCTATAGGAAACGCTGATGCAATTGATCCACTAA
TTTATGTCCTTGAGTCGGGGACCGCTGAAGCTAAAGAAAATTCTGCTGCC
ACACTTTTCAGTTTGTCAGTGATTGAGGATAACAAAGTCAAGATTGGGAG
ATCTGGTGCAATTCAACCTCTGGTTGATTTGTTGGGGCATGGAACTCCTA
GGGGAAAGAAAGATGCAGCCACAGCTTTGTTCAATTTGTCAATTTTTCAT
GAAAACAAGGCCCGCATTGTGCAGGCTGGTGCAGTGAAGTACCTTGTGGA
ACTGATGGACCCTGCAGCAGGCATGGTTGATAAAGCCGTTGCTGTTTTGT
CAAATCTTGCTACTATTCATGAGGGAAGGGCAGCAATTGGCCAGGAAGGA
GGTATTCCTGTCCTTGTTGAAGTTGTTGAACTGGGATCTGCAAGAGGGAA
GGAAAATGCAGCTGCTGCCCTTTTACAGCTTTGCACTAACAGCAGTAGAT
TTTGCAATATGGTACTCCAGGAAGGAGCTGTCCCACCGTTAGTGGCTTTG
TCACAGTCGGGCACCCCAAGAGCAAAGGAAAAGGCTCAAGCGCTTCTGAG
CTACTTCAGAAACCAACGACATGGCAATGGTGGTAGAGGATAACTGCGAA
AGTTTAAAGTGGTATGTCCTCTAATGTTTAAAGTAAGAGTCATACAGTGT
ACATTTGATGTTGCAAATAATGCATTTGAATGTTGTAGTTCTTTTATGTG
TGTACTTAATTTTAAAAAAGCCGGAGAAAGAAAGAAAAGAACTGATTTAA
GGGAGGCTTATTAGGCCCTTTGGTAGTGACTTTGTGAATTGTCAAACTTT
GTATATGTAGCTCAATTTTTGCAGCTTCTGTATGTATCTGGGGCCACAGA
TTATTTATATTTTAAAGAGAAAATATAGTTATGTGTTTTTAGTTTTCCCC
T

Sequence Length:

2801

Sequence Checksum:

331b85ef69c96c78a0121438e569fe27

View location in JBrowse:

DCARv2_Chr7:30467775..30475312+

Protein Sequence:

MATGAMEISKLKALLKNISGLFHLSSRDNLSFEPVQRYYQKVEEMFKVMK
LVLDAINDAEIASHESLQEPFASLYDSVDELREIFETWHPLMSKVYFVLQ
VESLMIKVRSSGLDIFEFLKSSDQPLPVELSTASLEHCLQKLKHLGLEQT
SAVITKATRDQVEGSGPTSDCLVKITDSLSLKSNQELLIEAVALEKLKEN
AEQAEKNVEVDYLDQLLALVTYMHERLVLLKQSESYNTVQIPADFCCPLS
LELMTDPVIVASGQTYERAFIRKWIDLGLTVCPKTRQVLAHTNLIPNYTV
KALVAHWCESNGVKLPDPMRSMNLNIPSSLLRHAASGAPRDSQTAPDSAY
SSGSPGNNFISSSVTNREGTSPSRPRSSSEDSLSEEAENGHALNIDSLSP
RRSENRQANLGDKNLDSGSRTTMSPTGEMPNVSRTNGSLSHGHNRTSSAS
STLSNANFSQGIPGDNNEASSLVTAYSIDDSGELTSERQSAATLSSAQRE
PEFSPRFETRSRTQSIWRRPSDRFVPRIVSSPAVETRAIPTAVEIQIQKM
VQDLKSTSMEEQRDATAELRLLAKHNMDNRIVIANCGGIPLLVNLLRSTD
ATTQENAVTALLNLSINDNNKAAIGNADAIDPLIYVLESGTAEAKENSAA
TLFSLSVIEDNKVKIGRSGAIQPLVDLLGHGTPRGKKDAATALFNLSIFH
ENKARIVQAGAVKYLVELMDPAAGMVDKAVAVLSNLATIHEGRAAIGQEG
GIPVLVEVVELGSARGKENAAAALLQLCTNSSRFCNMVLQEGAVPPLVAL
SQSGTPRAKEKAQALLSYFRNQRHGNGGRG

Relationship:

There are 2 relationships.
Relationships
The mRNA, XM_017363271.1, is a part of gene, LOC108196140.
The polypeptide, XM_017363271.1, derives from mRNA, XM_017363271.1.

Cross Reference:


NCBI Gene	108196140
NCBI Nuccore	XM_017363271.1

Gene:

LOC108196140

Model Evidence:

Supporting evidence includes similarity to: 2 ESTs, 13 Proteins, and 99% coverage of the annotated genomic feature by RNAseq alignments, including 25 samples with support for all annotated introns

Gbkey:

mRNA