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


Retrocopy-Parental alignment summary:






>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

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:

ParentalSTLFSLVHLRRLDLSDNDFNYSEIPHGVSQLSRLRILYLAGTSYS-GELPASMGKLSSLSELDISSCNFT
..L..L..L..LDLS.N.F...........L..L..L.......S.G.L.....KL.....L.....N..
RetrocopyTALGNLTQLTHLDLSSNSFK-GQLTSSLTNLIHLNFLDISRNDFSVGTLSWIIVKLTKFTALNLEKTNLI
ParentalGLVPSSLGHLTQLSYLDLSYNFFSGPIPSFLANLTTLTYLSLTSNNFSAGTLAWLGEQTKLTILYLDQIN
G....SL..LT.L.YL.L.YN...G.IP..L.NLT.L..L.L..NN..........E...L..L.L...N
RetrocopyGEILPSLSNLTGLTYLNLEYNQLTGRIPPCLGNLTLLKTLGLGYNNLEGPIPSSIFELMNLDTLIL-RAN
ParentalLNEGPIPMELHMLSNLKNLTDLQLSYNRISLLSYTSTNATLPKFKLLGLASCNLTEFPDFLQNQQELEVL
...G....EL.ML..LKNL..L.LS.N..SLL...S.N..LP...LLGLASCNL.EFP.FL.NQ.EL..L
RetrocopyKLSGTV--ELNMLVKLKNLHKLGLSHNDLSLLTNNSLNGSLPRLRLLGLASCNLSEFPHFLRNQDELKFL
ParentalILSTNKIHGPIPKWMWNISKETLEALFLSNNFLSGFSQVPDVLPWSRMSILELSSNMLQGSLPVPPSSTV
.LS.NKIHG.IPKWMWN..KETL....LSNN.L..F.Q.P.VLPW.....LELS.N.LQGSLPVPPSS..
RetrocopyTLSDNKIHGQIPKWMWNMGKETLWVMDLSNNLLTCFEQAPVVLPWITLRVLELSYNQLQGSLPVPPSSIS
ParentalEYSVSRNRLAGEIPSLICNLTSLSLLDLSGNNLSGSIPQCFTKLSSSLSILNLRRNNLNGPIPQTCTNTS
.Y.V..NRL.G..PSLIC.L..L..LDLS.NNLSG.IPQC....S.SLS.LNLR.NN..G.IPQT.T...
RetrocopyDYFVHNNRLNGKFPSLICSLHHLHILDLSNNNLSGMIPQCLSDSSDSLSVLNLRGNNFHGSIPQTFTSQC
ParentalNLRMIDLSENQLQGQIPKSLASCMMLEELVLGNNLINDIFPFWLGSLPRLQVLILRFNRFHGAIGSPKTN
.L.MID.S.NQL.GQIP.SL..C..LE.L.LGNN.IND.FPFWLGS.P.LQ.LILR.NRFHGAI..P..N
RetrocopyRLKMIDFSYNQLEGQIPRSLGNCKELEILNLGNNQINDTFPFWLGSFPELQLLILRHNRFHGAIENPRAN
ParentalFEFSKLRIIDLSYNGFTGNLPSEYLKNWDAMRIVDAENLTYIQVDEEFE-VPQYSWEEPYPFSTTMTNKG
FEF..L.IIDLSYN.F.GNLP..Y...W.AM..VD.EN..Y.Q....F.....Y...E.Y..S.TMTNKG
RetrocopyFEFPTLCIIDLSYNNFAGNLPAGYFLTWVAMSRVDEENFSYMQSMTGFVLIRTYRLYENYNYSMTMTNKG
ParentalMTREYELIPDILIAIDLSSNRFHGEIPESIGNPNGLRWLNLSNNALIGAIPTSLANLTLLEALDLSQNKL
M.R.Y..IP....AIDLSSN.F.GEIP.SIG...GL..LN.S.N.L.G.IP..L.NL..LEALDLSQN.L
RetrocopyMERVYPKIPRSFKAIDLSSNKFIGEIPKSIGKLRGLHLLNISSNSLTGHIPSFLGNLAQLEALDLSQNNL
ParentalSREIPQQLVQLTFLAFFNVSHNHLTGPIPQGKQFATFSRASFDGNPGLCGSPLSRACGSSEQSPPTPSSS
S.EIPQQL...TFL.FFNVSHNHL.GPIPQGKQF.TF...S..GNPGLCG.PLS..C..S....P.P...
RetrocopySGEIPQQLKGMTFLEFFNVSHNHLMGPIPQGKQFNTFQNDSYEGNPGLCGNPLSKECENSKSTAPPPPTD
ParentalKQGSTSEFDWK----FVLMGCGSGLVIGVSIGYCLTSWKHEWFVKTFGKQHTK
K.G...E...K.....VLMG.GSGLV.G..IGY.LT..KHEWFVKTFGK...K
RetrocopyKHGGDLESGRKVELMIVLMGYGSGLVVGMAIGYTLTTRKHEWFVKTFGKRQRK

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Vitis vinifera was not studied using ChIP-Seq data.

EST - click to see more details

Vitis vinifera was not studied using EST data.

TSS - click to see more details

Vitis vinifera was not studied using FANTOM5 data.

Lab - click to see more details

retro_vvin_1 was not experimentally validated.

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.
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 ,


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