RetrogeneDB ID: retro_vvin_2

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 8:18390357..18391452(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_08s0007g04440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_04s0023g00140
• Aliases: None
• Description: None

Sequence

>retro_vvin_2
ATGAAGCTGGTAGAAGAAGAAAAAATCCTTCCTAATAGCAGTGGAATCATCAATATCGTTCCTGAAGAACCAGATGACAT
GTGGCTCCTCTACAATTTGATTTCTAAGGGCGATGTCATCGTTGCCGATACAACCCGCAAAACCGCCTTTGGCAGAGTTA
GACTCACACTTGAAATCAAAATCACCGCCATCGATTATGATAAAGTAGGCTCAGTAATCCGCGTCGCCGGCAGGAACTTG
GTGCACAATGAACACGTAGACGCCGGTGCCTTCCACACCATAGAGATTGAGAGGAATAAACCGTTTGACCTGAAGAAGAA
AGTTTGGGATTCTGATGCAATCGAGGAACTACGCTCCTACGGCAATGCTGCTAAAGCAGACCTCGCAGTCTTGTTGATAC
AAGACGTATCCGCGGAGTTGTACTCGATAGGGAAAATAGCCACTACACTTTGTGCCAACATTGAAGCCCCATCTAAAACC
AATAGAGCTGCAAAATCGAAATCTCAGTCAAAGTCAAACAAGTTTTTTGAAAACATTTTAACAGAATTTGTAAAGCACGT
AAATTTCAACTTCGTAAGCTTGGTCATAATAGCAAGTCCTGTTGGGACGGAGTTTCGGCAATACTTGCTAGCAGAATCAC
GAAGGCAGAAGCTGCAGCAAATAGAAGAAAATAAGGAACGTGTGGTAGTGGTGAATACTTCGGGAAAAGCAACTTTGAAA
GCGGTGTTGCAAGAGCCCGAGGTAATGAAATTGATTCGGGGCAAAAACGGGGCAGTGGAGATAACAGCATGGAAGGATTT
GTGCGACATGTTGAGCAACGATTCAAGTAGGGCGTGTTATGGATCAAAGAGTGTGGAGAAGGCAAATGAATTGATGGCAA
TCGACACCCTGTTTATAAGTGATGAACTTTACCGGAGTGCAAACCATGGAAGTAGGCACAAGTACACGGATTTAGTTAAG
TCGGTAAAGAAGGCGGGAGGGAAGGCCTTGGTATATTCACACAATCATGTAATGGGAGAGCAGTTAGGTCAGTTAACTGG
GATTGCTGCTATTCTTAGGTTTCCATTGCCTGATCTGGATGACATGGAATTGTGA

Alignment

ORF - retro_vvin_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.47 %
• Parental protein coverage: 84.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVKLKLEIKVEVADYDKVGSVLRIRGKNILENEYVKIGQFHTLEIEQHRPFVLRKVVWDSLALDTLNQAS
          RV.L.LEIK....DYDKVGSV.R..G.N...NE.V..G.FHT.EIE...PF.L.K.VWDS.A...L....
Retrocopy RVRLTLEIKITAIDYDKVGSVIRVAGRNLVHNEHVDAGAFHTIEIERNKPFDLKKKVWDSDAIEELRSYG

Parental  DPAASADLAVVLMQEGLAHVILIGRSLTITRSRIEASIPRKHGPAIAGYEAALNKFFENVLQAFLKYVDF
          ..AA.ADLAV.L.Q...A....IG...T.....IEA........A........NKFFEN.L..F.K.V.F
Retrocopy N-AAKADLAVLLIQDVSAELYSIGKIATTLCANIEAP-SKTNRAAKSKSQSKSNKFFENILTEFVKHVNF

Parental  NVVRCAVIASPGFTKDQFHRHLLLEAERRQLRSIIENKSRIILVHTSSGYKHSLKEVLDAPNVMNMIKDT
          N.V....IASP..T...F...LL.E..R..L..I.ENK.R...V.TS...K..LK.VL..P.VM..I...
Retrocopy NFVSLVIIASPVGT--EFRQYLLAESRRQKLQQIEENKERVVVVNTSG--KATLKAVLQEPEVMKLIRGK

Parental  KAAQEVQALKDFFNMLSNDPARACYGPKHVEVAHERMAVQTLLITDDLFRSADIPTRQKYVNFVNSVKDS
          ..A.E..A.KD...MLSND..RACYG.K.VE.A.E.MA..TL.I.D.L.RSA....R.KY...V.SVK..
Retrocopy NGAVEITAWKDLCDMLSNDSSRACYGSKSVEKANELMAIDTLFISDELYRSANHGSRHKYTDLVKSVKKA

Parental  GGTAHIFSSMHVSGEQLAQLTGIAAILRFPLPDLEDIEM
          GG.A...S..HV.GEQL.QLTGIAAILRFPLPDL.D.E.
Retrocopy GGKALVYSHNHVMGEQLGQLTGIAAILRFPLPDLDDMEL

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_2 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Aegilops tauschii	F775_08238	1 retrocopy	retro_atau_9,
Hordeum vulgare	MLOC_5075	1 retrocopy	retro_hvul_86,
Hordeum vulgare	MLOC_54416	1 retrocopy	retro_hvul_87,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2 ,