RetrogeneDB ID: retro_vvin_147

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 4:20437662..20438149(+)
• Located in intron of: VIT_04s0210g00040

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_18s0001g12300
• Aliases: None
• Description: None

Sequence

>retro_vvin_147
ATGGAAAACTATCAACATTCAGAGCCTCAACACGGTCTTGAAAGCTTTTCTACCAGAGAAACAATTTCTCTTAACTTCTT
AGAAAAGGCTACGTCAGGCTATGAATTCCATCGACCAGAGAGATAACCTGGGACCTTACAAATGTCAAATTAAGTTACGC
TTTGCAAAACGGACTAAGGGTAGAACTTCATCAGCATAACCAGATTTCGTGAGAGATGAAGTAGATATTGGTCCGAGAGG
GTATGAACAAAGCAGTAGAAATGAAGTCACTATTATTTCCAGGCAGAGCATCAGGAGAGGAAAGAATAATATGAAAGGTT
CCTATCCAACGGGCATTCTCAAGGTTCCCAGCTTTCTCATGGGCTATCACATCTTAACAATACGTGTACTTCCAGCCAAA
ATTATTCAGAGTGTTACTACATTTTCACAGAGACAGATGCATGACGTGGAATGTCTCGCAACAAAGCTCACGAGAGGGTT
GAAATCC

Alignment

ORF - retro_vvin_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.48 %
• Parental protein coverage: 58.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENYQHSELQHGPERLFSTRKAISP-TSQERLCRAMNSIDLCDNLEPYECKIKLRFAKRTEGRTSSAEPD
          MENYQHSE.QHG.E..FSTR..IS..TS..RL..AMNSID..DNL.PY.C.IKLRFAKRT.GRTSSA.PD
Retrocopy MENYQHSEPQHGLES-FSTRETISL>TS*KRLRQAMNSIDQRDNLGPYKCQIKLRFAKRTKGRTSSA*PD

Parental  FVGDEVDIGPGGPEQSSRNEVTVISKQSIRRRKNDMKGSHPKGILKVPQLSRGLPHLSNTCTSSQSYSQS
          FV.DEVDIGP.G.EQSSRNEVT.IS.QSIRR.KN.MKGS.P.GILKVP....G..H............QS
Retrocopy FVRDEVDIGPRGYEQSSRNEVTIISRQSIRRGKNNMKGSYPTGILKVPSFLMGY-HILTIRVLPAKIIQS

Parental  AISFSQRQMHDIECLAAKLTRELKS
          ...FSQRQMHD.ECLA.KLTR.LKS
Retrocopy VTTFSQRQMHDVECLATKLTRGLKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vitis vinifera was not studied using RNA-Seq expression data.

ChIP-Seq

Vitis vinifera was not studied using ChIP-Seq data.

EST

Vitis vinifera was not studied using EST data.

TSS

Vitis vinifera was not studied using FANTOM5 data.

Lab

retro_vvin_147 was not experimentally validated.

Homology

Retrocopy orthology:

Vitis vinifera does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_18s0001g12300	3 retrocopies	retro_vvin_147 , retro_vvin_174, retro_vvin_61,