RetrogeneDB ID: retro_vvin_1

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 12:9266350..9268609(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_12s0057g00620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_12s0057g00800
• Aliases: None
• Description: None

Sequence

>retro_vvin_1
ATGGGGATTTTCAAGCTGCCAAGCTTAGAACTCCTTGATCTGATGTCTAATAGATATCTGACTGGCCATTTGCCTGAATT
TCACAATGCTAGTCACCTCAAATATTTGGATCTCTATTGGACAAGTTTCTCTGGTCAGCTACCAGCTTCCATTGGATTCC
TTAGTTCCTTGAAGGAATTGGATATCTGCTCATGCAATTTCAGTGGGATGGTTCCAACTGCACTCGGCAACCTTACCCAG
CTTACCCACCTGGACCTTTCAAGTAACTCATTTAAGGGTCAGCTCACCTCTTCATTGACCAACCTTATCCATCTCAATTT
CTTGGATATTTCTAGGAATGATTTCAGTGTTGGGACCTTGTCTTGGATTATTGTCAAGCTGACCAAATTCACTGCTTTGA
ACCTTGAAAAGACCAATTTAATTGGTGAGATCTTGCCTTCTCTTTCAAACCTAACTGGACTGACTTATTTAAACCTGGAG
TATAATCAACTTACTGGTAGAATTCCACCATGCCTTGGGAACCTGACCCTGTTAAAAACCTTAGGTCTTGGGTACAATAA
TTTGGAAGGTCCAATACCAAGCTCAATATTTGAACTGATGAACCTTGATACTCTCATTCTACGTGCAAACAAGTTGAGTG
GCACAGTGGAGCTGAACATGCTTGTTAAGCTCAAAAATCTCCACAAACTCGGCTTGTCTCATAACGATCTATCATTGCTC
ACTAACAACAGTCTCAATGGTTCTCTTCCAAGGCTTAGGCTTTTAGGATTAGCTTCATGCAACTTGAGCGAGTTCCCACA
TTTCCTAAGGAACCAAGATGAATTGAAGTTTTTAACACTTTCTGACAACAAAATTCATGGCCAAATACCAAAGTGGATGT
GGAACATGGGTAAAGAAACTCTTTGGGTCATGGACCTATCTAACAACTTATTAACCTGCTTCGAGCAGGCCCCAGTTGTC
CTTCCATGGATTACTCTACGAGTTCTAGAGCTTAGTTATAATCAGCTACAAGGGTCCCTTCCAGTTCCACCATCTTCCAT
CTCTGATTATTTTGTCCATAACAACAGACTAAATGGAAAATTTCCGTCGTTGATTTGCAGCTTGCATCATCTTCACATTC
TTGATTTGTCGAATAACAACTTAAGTGGCATGATTCCTCAATGTTTGAGCGACTCCAGCGATTCTCTATCAGTGTTGAAT
CTACGAGGCAACAACTTTCATGGGAGCATTCCTCAAACATTCACCAGCCAATGCAGATTAAAGATGATTGATTTTAGTTA
CAATCAGTTAGAGGGGCAGATACCAAGATCATTGGGCAATTGTAAAGAGCTTGAGATTCTGAATCTTGGAAACAATCAGA
TCAATGATACGTTCCCCTTTTGGTTGGGATCTTTTCCAGAGTTGCAACTTCTCATTTTGCGGCATAACAGATTTCATGGC
GCAATCGAGAATCCTAGAGCCAACTTTGAGTTCCCCACGCTGTGTATCATTGACCTCTCGTACAATAATTTTGCAGGAAA
TTTGCCAGCAGGCTACTTTCTCACATGGGTGGCCATGAGCAGGGTCGATGAAGAGAATTTTTCATATATGCAGTCAATGA
CGGGATTTGTCCTAATCCGAACATATCGGCTTTATGAAAACTACAATTACTCAATGACAATGACGAACAAAGGCATGGAA
AGGGTGTACCCGAAGATCCCTCGCAGTTTTAAAGCAATTGATCTCTCAAGCAACAAATTTATAGGAGAGATCCCAAAATC
CATTGGGAAACTCAGGGGACTTCATTTGCTCAACATTTCCTCCAACAGTCTTACTGGTCACATCCCATCTTTTCTTGGGA
ACTTAGCACAGCTTGAGGCACTGGACCTATCTCAAAACAATCTCTCAGGAGAGATCCCTCAGCAGCTAAAGGGAATGACA
TTCCTTGAGTTCTTCAATGTTTCTCACAATCATCTCATGGGACCTATACCGCAAGGGAAGCAATTTAATACATTTCAGAA
CGACTCATACGAGGGAAATCCAGGATTGTGCGGAAATCCTTTGTCAAAGGAGTGTGAAAACTCTAAGTCAACAGCACCAC
CACCACCAACCGACAAACATGGAGGGGACTTGGAGAGTGGCCGCAAAGTTGAGTTGATGATAGTATTGATGGGATATGGA
AGTGGTCTGGTAGTTGGAATGGCAATTGGTTACACCTTAACCACAAGGAAACATGAATGGTTTGTCAAGACTTTCGGCAA
GAGGCAGAGAAAGTGTTGA

Alignment

ORF - retro_vvin_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.34 %
• Parental protein coverage: 84.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STLFSLVHLRRLDLSDNDFNYSEIPHGVSQLSRLRILYLAGTSYS-GELPASMGKLSSLSELDISSCNFT
          ..L..L..L..LDLS.N.F...........L..L..L.......S.G.L.....KL.....L.....N..
Retrocopy TALGNLTQLTHLDLSSNSFK-GQLTSSLTNLIHLNFLDISRNDFSVGTLSWIIVKLTKFTALNLEKTNLI

Parental  GLVPSSLGHLTQLSYLDLSYNFFSGPIPSFLANLTTLTYLSLTSNNFSAGTLAWLGEQTKLTILYLDQIN
          G....SL..LT.L.YL.L.YN...G.IP..L.NLT.L..L.L..NN..........E...L..L.L...N
Retrocopy GEILPSLSNLTGLTYLNLEYNQLTGRIPPCLGNLTLLKTLGLGYNNLEGPIPSSIFELMNLDTLIL-RAN

Parental  LNEGPIPMELHMLSNLKNLTDLQLSYNRISLLSYTSTNATLPKFKLLGLASCNLTEFPDFLQNQQELEVL
          ...G....EL.ML..LKNL..L.LS.N..SLL...S.N..LP...LLGLASCNL.EFP.FL.NQ.EL..L
Retrocopy KLSGTV--ELNMLVKLKNLHKLGLSHNDLSLLTNNSLNGSLPRLRLLGLASCNLSEFPHFLRNQDELKFL

Parental  ILSTNKIHGPIPKWMWNISKETLEALFLSNNFLSGFSQVPDVLPWSRMSILELSSNMLQGSLPVPPSSTV
          .LS.NKIHG.IPKWMWN..KETL....LSNN.L..F.Q.P.VLPW.....LELS.N.LQGSLPVPPSS..
Retrocopy TLSDNKIHGQIPKWMWNMGKETLWVMDLSNNLLTCFEQAPVVLPWITLRVLELSYNQLQGSLPVPPSSIS

Parental  EYSVSRNRLAGEIPSLICNLTSLSLLDLSGNNLSGSIPQCFTKLSSSLSILNLRRNNLNGPIPQTCTNTS
          .Y.V..NRL.G..PSLIC.L..L..LDLS.NNLSG.IPQC....S.SLS.LNLR.NN..G.IPQT.T...
Retrocopy DYFVHNNRLNGKFPSLICSLHHLHILDLSNNNLSGMIPQCLSDSSDSLSVLNLRGNNFHGSIPQTFTSQC

Parental  NLRMIDLSENQLQGQIPKSLASCMMLEELVLGNNLINDIFPFWLGSLPRLQVLILRFNRFHGAIGSPKTN
          .L.MID.S.NQL.GQIP.SL..C..LE.L.LGNN.IND.FPFWLGS.P.LQ.LILR.NRFHGAI..P..N
Retrocopy RLKMIDFSYNQLEGQIPRSLGNCKELEILNLGNNQINDTFPFWLGSFPELQLLILRHNRFHGAIENPRAN

Parental  FEFSKLRIIDLSYNGFTGNLPSEYLKNWDAMRIVDAENLTYIQVDEEFE-VPQYSWEEPYPFSTTMTNKG
          FEF..L.IIDLSYN.F.GNLP..Y...W.AM..VD.EN..Y.Q....F.....Y...E.Y..S.TMTNKG
Retrocopy FEFPTLCIIDLSYNNFAGNLPAGYFLTWVAMSRVDEENFSYMQSMTGFVLIRTYRLYENYNYSMTMTNKG

Parental  MTREYELIPDILIAIDLSSNRFHGEIPESIGNPNGLRWLNLSNNALIGAIPTSLANLTLLEALDLSQNKL
          M.R.Y..IP....AIDLSSN.F.GEIP.SIG...GL..LN.S.N.L.G.IP..L.NL..LEALDLSQN.L
Retrocopy MERVYPKIPRSFKAIDLSSNKFIGEIPKSIGKLRGLHLLNISSNSLTGHIPSFLGNLAQLEALDLSQNNL

Parental  SREIPQQLVQLTFLAFFNVSHNHLTGPIPQGKQFATFSRASFDGNPGLCGSPLSRACGSSEQSPPTPSSS
          S.EIPQQL...TFL.FFNVSHNHL.GPIPQGKQF.TF...S..GNPGLCG.PLS..C..S....P.P...
Retrocopy SGEIPQQLKGMTFLEFFNVSHNHLMGPIPQGKQFNTFQNDSYEGNPGLCGNPLSKECENSKSTAPPPPTD

Parental  KQGSTSEFDWK----FVLMGCGSGLVIGVSIGYCLTSWKHEWFVKTFGKQHTK
          K.G...E...K.....VLMG.GSGLV.G..IGY.LT..KHEWFVKTFGK...K
Retrocopy KHGGDLESGRKVELMIVLMGYGSGLVVGMAIGYTLTTRKHEWFVKTFGKRQRK

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_1 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_12s0057g00800	1 retrocopy	retro_vvin_1 ,