RetrogeneDB ID: retro_vvin_4

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 5:17616324..17617125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_05s0029g01470
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_13s0067g00420
• Aliases: None
• Description: None

Sequence

>retro_vvin_4
ATGAGTTCCTGGAATGACTCACTGCATTTCTGTCAGTGGCAGGGGGTTACATGCAGTCGCCGACGTCAGAGGGTCACAGC
CTTGAGGTTGGAGGGTCAGAGCTTAGCTGGTTCCTTACCTCCTATTGGGAACTTAACATTCCTGAGAGAGTTGGTGTTGT
CCAACAATAACTTGCAGGGTTCTATCCCCACTGACATTGGTCTTTTGCGACGAATGCAGCATCTCAATCTCAGCACAAAT
TCTCTCCAAGGTGAGATTCCCATTGAGCTGACCAACTGTTCAAACCTCAAGACTGTGGACTTAACAAGGAACAATCTGAC
CGGGCAGATTCCCTTGCACGTTGGCCATATGTTGAAACTCCTACTTCTATGGCTTGGTGCCAACGATCTAACAGGGGTTG
TCCCATTTACTTTGGGAAACCTGTCATCTCTTCAACATCTGTCCGTTGCGTACAATCATTTGGAGGGAAATATTCCACAT
GAATTAGGTCGTTTGAAGAGCTTGAAATATTTATATTTGGATGTAAATAACCTATCTGGTATGATTCTTCCCTCACTCTA
TAATTGGTCATCTCCCATTGAATTTTTTGTATCTGGCAACATTCTAACTGGAAATTTTACTCCAAACATGAGGTTTAATT
TTCCTCAACTCCGCAAGTTTGGCATAGCAGGGAATCAGTTTACCGGAGTAATTCCAGATACACTATCCAATATTTCAGGA
CTTGAACATTTGGATCTAGGTAACAATTATCTAACTGGCCAAGTCCCTGATAGCTTAGGAGTGCTCAAGGATCTCTATTG
A

Alignment

ORF - retro_vvin_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.71 %
• Parental protein coverage: 55.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSWNDSLHFCQWQGVTCSRRHQRVTVLRLEGQSLAGSLPPIGNLTFLRELVLSNNNLQGSIPTDIGLLR
          .SSWNDSLHFCQWQGVTCSRR.QRVT.LRLEGQSLAGSLPPIGNLTFLRELVLSNNNLQGSIPTDIGLLR
Retrocopy MSSWNDSLHFCQWQGVTCSRRRQRVTALRLEGQSLAGSLPPIGNLTFLRELVLSNNNLQGSIPTDIGLLR

Parental  RLQHLNLSTNSLQGEIPVELTNCSNLITVDLTRNNLTGQIPFPFGHMSKLLILRLGRNSVNNLSGMIPSS
          R.QHLNLSTNSLQGEIP.ELTNCSNL.TVDLTRNNLTGQIP...GHM.KLL.L.LG.N....L.G..P..
Retrocopy RMQHLNLSTNSLQGEIPIELTNCSNLKTVDLTRNNLTGQIPLHVGHMLKLLLLWLGAN---DLTGVVPFT

Parental  LYNLSSAIELVFTANRLSGNFMSSMRFSLPQLLRFAIAQNQFIGIIPDILSNISGLELLDVGENYLTGQ-
          L.NLSS...L....N.L.GN........L..L.......N...G.I...L.N.S......V..N.LTG..
Retrocopy LGNLSSLQHLSVAYNHLEGNIPHELG-RLKSLKYLYLDVNNLSGMILPSLYNWSSPIEFFVSGNILTGNF

Parental  VPDIG-NLINLTTFGVAQNDFTGVIPTSIGKLQNLRQLELSWNRLSGLLPSSLGNLSQL
          .P....N...L..FG.A.N.FTGVIP........L..L.L..N.L.G..P.SLG.L..L
Retrocopy TPNMRFNFPQLRKFGIAGNQFTGVIPDTLSNISGLEHLDLGNNYLTGQVPDSLGVLKDL

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_4 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_13s0067g00420	1 retrocopy	retro_vvin_4 ,