RetrogeneDB ID: retro_vvin_49

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:13770276..13771112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0008g00770
• Aliases: None
• Description: None

Sequence

>retro_vvin_49
ACTGCTGCTTTGTGCTCTCTGTAACGGTCCATTTGGATTAAAGGGTTCAGTTTCGCTCCAAGTGGGTCTACTGACCATGG
GATTCGACATCCAATTAAACTGAACTCGGCTAAGCCATGCAGATCTTATATCGAAAGAAGCTTGATTACTGGGAAGTTAC
TTTCCTTTGTGTCTATCATTGTGCCTGAAAATGGAGGAAGCGAAGTCAGTTGTATTGACTATGGCCTGAATGCAGCTGGT
CATGAAGTGTGTGTAATTATTTACAAAGAAAAACAACGATAAATGAAGATATTAGAACTCATTTGCTTCAGAGAATTTCA
TATCCCGAGCAGTGATGGAAGTTGTTAGCTCTTGCCTCACAAACAAATATTCTTAGGGATTGTCTGGTAGAGGATACTAT
GGCGGCAATGAATTCTTTGATGAGCTAGAAATCCTCTGTCAGAAGAGGGCTTTGGCAGTATTCCACCTAAAGGGAAAGAC
GTGAGGCGTCAATGTTCAACCATTGTCAGTTTCTCCAGCTACCTTTGAAGTATGCACTGTCCTTCTCAATCTACATGGCA
TGATCATAGGCTTGGACTTACCTCGTAAGGCCACTTGTCTCATAGTTTCATAGCTCCTAAAAGACGGATATCAGGCACCT
CAATTTATTGTGAGTCTAGGCCCCAACGACTCGATGAATCTACAGGTCTTGGTCTTGCTGTTTATGACATGCTTGAGAAG
AAACTAATCTATTGAGACCAAAACTTCTTATTGTTGATGGCAGTGTTTATCCTTGAGATTTTGATTATCCTCGAGTGAGG
AAGATGGCAAACGGCGTTGGTGCTTTTCTCATGCTG

Alignment

ORF - retro_vvin_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.57 %
• Parental protein coverage: 52.46 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAAMGSLQQPIWIKGSSFAPNGSTVNGFPHQIKLNSVKPCRSYIKGSLVTGKPPSSVSVTVPGNGDSGVN
          TAA..SL...IWIKG.SFAP.GST..G..H.IKLNS.KPCRSYI..SL.TGK..S.VS..VP.NG.S.V.
Retrocopy TAALCSL*RSIWIKGFSFAPSGSTDHGIRHPIKLNSAKPCRSYIERSLITGKLLSFVSIIVPENGGSEVS

Parental  FIDHGLNEADPEVCAIIYKEKQRQMKSLELI-ASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGGNEFI
          .ID.GLN.A..EVC.IIYKEKQR.MK.LELI.ASENF.SRAVME.V.SCLTNKYS.GL.G..YYGGNEF.
Retrocopy CIDYGLNAAGHEVCVIIYKEKQR*MKILELI>ASENFISRAVMEVVSSCLTNKYS*GLSGRGYYGGNEFF

Parental  DELETLCQKRALAAFHLDGKKWGVNVQPLSGSPANFEVYTALLNPHDRIMGLDLPHG-GHLSHGFMTPKR
          DELE.LCQKRALA.FHL.GK..GVNVQPLS.SPA.FEV.T.LLN.H..I.GLDLP...GHLSH.F..PKR
Retrocopy DELEILCQKRALAVFHLKGKT*GVNVQPLSVSPATFEVCTVLLNLHGMIIGLDLPRK<GHLSHSFIAPKR

Parental  RVSGTSIYFESMPYRLDEST--GLVDYDMLEK-TANLFRPKLIIAGASAYPRDFDYPRMRKIADGVGAFL
          R.SGTSIY.ES.P.RLDEST..GL..YDMLEK...NL.RPKL.I...S.YP.DFDYPR.RK.A.GVGAFL
Retrocopy RISGTSIYCESRPQRLDESTGLGLAVYDMLEK<ETNLLRPKLLIVDGSVYP*DFDYPRVRKMANGVGAFL

Parental  MM
          M.
Retrocopy ML

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_49 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400029389	1 retrocopy	retro_stub_40,
Vitis vinifera	VIT_04s0008g00770	1 retrocopy	retro_vvin_49 ,