RetrogeneDB ID: retro_vvin_44

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:8474512..8477101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_10s0003g04830
• Aliases: None
• Description: None

Sequence

>retro_vvin_44
AATTGTGTTGCAGGAGAAATACCTCAATCACTATTCAACATCTATTCGTTAAGGTTTTTGAATTTGGAAATAAATAACCT
AGAAGGTGAAATCTCTAGTTTTTCTCATTGTCGAGAGCTTCGAGTGCTAAAATTATCAATCAATCAATTCACTGGAGGCA
TTCCAAAAGCCCTAGGGAGTTTGTCTGATCTTGAAGAATTATATCTTGGTTATAACAAATTGACAGGTGGAATTCCTAGA
GAGATTGGGATTCTTTCAAATTTAAATATTTTGCACTTAGCGTCTAGTGGAATCAATGGCCCTATTCCTGCCGAAATTTT
CAATATCTCTTCATTGCACAGGATTGATTTCACTAATAATAGCCTTTCGGGGGGTCTTCCAATGGATATTTGTAAACATC
TTCCTAATCTCCAAGGGCTCTATCTTTCTCAGAATCATCTCAGTGGTCAACTTCCTACAACTCTATTTTTATGTGGAGAG
CTCCTGTTACTGTCATTATCAATCAATAAATTCACAAGAAGCATACCAAGAGATATTGGCAACTTATCAAAGCTTAAAAA
GATCTATCTAAGCACCAATAGCCTCATAGGTTCCATTCCAACTTCATTTGGTAATTTGAAGGCCTTAAAATTCCTTCAGT
TGGGGTCCAACAATCTTATAGGGACGATACCAGAAGATATTTTTAACATCTCTAAACTACAGACCCTTGCGTTGGCGCAA
AATCACCTTTCAGGCGGTCTTCCATCAAGTATTAGCACTTGGCTCCCAGATCTTGAAGGGCTTTTTATAGGAGGCAATGA
ATTCAGTGGAACAATTCCAGTGTCTATTTCAAATATGTCAAAACTTATCCGGCTACACATATCGGACAACTATTTCATTG
GTAATGTGCCAAAAGATCTCAGTAACCTAAGGAAGCTTGAAGTTCTCAACCTTGCAGGCAATCAATTGACTGATGAACAC
TTAACCTCTGAGGTTGGTTTTCTTACTTCTTTGACAAATTGCAAATTTTTGAGAACATTGTGGATAGATTATAATCCTTT
AAAAGGCACTCTTCCAAATTCACTAGGGAATCTTTCCGTTGCTCTTGAAAGTTTTACAGCATCAGCCTGCCATTTCAGAG
GAACCATTCCCACAGGAATTGGTAATTTGACCAATTTGATATGGCTGGACCTGGGAGCTAATGACTTAACAGGGTCGATT
CCAACTACATTGGGACAGCTACAGAAGCTCCAACGATTGTACATTGCTGGAAATAGAATACAAGGATCCATTCCAAATGA
TCTTTTCCATTTGAAGAACTTGGGATACTTGCATTTGAGTTCTAACAAATTGTCTGGATCAATCCCAAGTTGTTTTGGAG
ATCTTCCTGCGCTACGAGAACTCTCTCTTGACTCCAATGTGTTAGCTTTCAACATTCCTATGTCCTTTTGGAGCCTTAGA
GATTTGTTGGTTCTTAGCTTGTCTTCAAATTTCTTGACTGGTAATCTACCTCCCGAAGTTGGAAACATGAAGTCCATTAC
AACATTGGACCTGTCAAAGAACCTTATTTCAGGTTACATTCCAAGAAGGATGGGAGAACTACAAAATTTGGTTAATCTTT
GCTTGTCCCAAAACAAACTACAAGGCTCAATACCTGTAGAATTTGGTGATTTGCTAAGCTTGGAATCCATGGATCTATCT
CAGAACAATTTATCTGGAACCATTCCCAAGTCATTGGAGGCCCTTATTTATCTCAAGCATCTAAATGTTTCTTTCAATAA
ACTACAAGGAGAAATTCCGGATGGAGGACCTTTCGTAAATTTCACTGCTGAATCGTTCATCTTCAATGAAGCCTTATGTG
GAGCACCTCATTTTCAAGTCATAGCATGTGATAAAAACAACCACACTCAATCATGGAAGACAAAGTCATTCATCTTGAAA
TATATTCTACTACCAGTCGGATCAATAGTAACTTTAGTGGCTTTCATTGTTCTGTGGATACGTAGACAAGATAACACGGA
AATACCAGCTCCAATTGATTCATGGCTTCCTGGAGCACATGAAAAAATTTCACAGCAGCAACTTCTTTATGCAACAAACG
ACTTTGGTGAAGACAATTTGATTGGGAAAGGAAGCCTAGGCATGGTATACAAAGGGGTATTATCTAATGGCTTAACTGTT
GCTATAAAGGTTTTCAATTTAGAATTCCAAGGAGCCTTGAGGAGTTTCGATTCAGAATGTGAAGTGATGCAAGGGATCTG
CCACCGAAATCTTATCAGGATAATTACCTGTTGCTCAAACCTTGATTTCAAAGCATTGGTGCTCGAATATATGCCTAAAG
GAAGTCTTGATAAGTGGTTGTATTCTCATAACTATTTTTTGGATCTCTTCCAAAGATTAAATATTATGATTGATGTAGCA
TTGGCATTGGAGTATCTTCATCATGATTGTTCGAGCCTTGTGGTGCATTGCGACTTGAAGCCCAGTAATGTTTTGTTAGA
TAACAACATGGTTGCTCATGTGGCTGATTTTGGGATTGCAAGACTCTTAACTGAAACAGAGTCTATGCAGCAAACAAAGA
CCTTGGGCACAATAGGCTATATGGCACCA

Alignment

ORF - retro_vvin_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NQLIGEIPKKMSNLLNLKVLSFPMNNLTGSIPTTIFNMSSLLNISLSYNSLSGSLPMDICYANLKLKELN
          N...GEIP....N...L..L....NNL.G.I.........L....LS.N...G..P.........L.EL.
Retrocopy NCVAGEIPQSLFNIYSLRFLNLEINNLEGEI-SSFSHCRELRVLKLSINQFTGGIPKALGSLS-DLEELY

Parental  LSSNHLSGKVPTGLGQCIKLQGISLSCNDFTGSIPSGIGNLVELQSLSLQNNSLTEG-EISSFSHCRELR
          L..N.L.G..P...G....L....L......G.IP..I.N...L......NNSL..G.......H...L.
Retrocopy LGYNKLTGGIPREIGILSNLNILHLASSGINGPIPAEIFNISSLHRIDFTNNSLSGGLPMDICKHLPNLQ

Parental  VLKLSINH--GQLPTTLFLCGELLLLSLSINKFTGSIPRDIGNLSKLEKIYLSTNSLIGSIPTSFGNLKA
          .L.LS.NH..GQLPTTLFLCGELLLLSLSINKFT.SIPRDIGNLSKL.KIYLSTNSLIGSIPTSFGNLKA
Retrocopy GLYLSQNHLSGQLPTTLFLCGELLLLSLSINKFTRSIPRDIGNLSKLKKIYLSTNSLIGSIPTSFGNLKA

Parental  LKFLQLGSNNLTGTIPEDIFNISKLQTLALAQNHLSGGLPSSIGTWLPDLEGLFIGGNEFSGTIPVSISN
          LKFLQLGSNNL.GTIPEDIFNISKLQTLALAQNHLSGGLPSSI.TWLPDLEGLFIGGNEFSGTIPVSISN
Retrocopy LKFLQLGSNNLIGTIPEDIFNISKLQTLALAQNHLSGGLPSSISTWLPDLEGLFIGGNEFSGTIPVSISN

Parental  MSKLIRLHISDNYFTGNVPKDLSNLRKLEVLNLAGNQLTDEHLTSEVGFLTSLTNCKFLRTLWIDYNPLK
          MSKLIRLHISDNYF.GNVPKDLSNLRKLEVLNLAGNQLTDEHLTSEVGFLTSLTNCKFLRTLWIDYNPLK
Retrocopy MSKLIRLHISDNYFIGNVPKDLSNLRKLEVLNLAGNQLTDEHLTSEVGFLTSLTNCKFLRTLWIDYNPLK

Parental  GTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLGHLQKLQRLYIAGN
          GTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLG.LQKLQRLYIAGN
Retrocopy GTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLGQLQKLQRLYIAGN

Parental  RIQGSIPNDLCHLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDLMVLSLS
          RIQGSIPNDL.HLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDL.VLSLS
Retrocopy RIQGSIPNDLFHLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDLLVLSLS

Parental  SNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRMGELQNLVNLCLSQNKLQGSIPVEFGDLLSLESMD
          SNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRMGELQNLVNLCLSQNKLQGSIPVEFGDLLSLESMD
Retrocopy SNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRMGELQNLVNLCLSQNKLQGSIPVEFGDLLSLESMD

Parental  LSQNNLFGTIPKSLEALIYLKHLNVSFNKLQGEIPNGGPFVNFTAESFIFNEALCGAPHFQVIACDKNNR
          LSQNNL.GTIPKSLEALIYLKHLNVSFNKLQGEIP.GGPFVNFTAESFIFNEALCGAPHFQVIACDKNN.
Retrocopy LSQNNLSGTIPKSLEALIYLKHLNVSFNKLQGEIPDGGPFVNFTAESFIFNEALCGAPHFQVIACDKNNH

Parental  TQSWKTKSFILKYILLPVGSAVTLVAFIVLWIRRRDNTEIPAPIDSWLPGAHEKISQQQLLYATNGFGED
          TQSWKTKSFILKYILLPVGS.VTLVAFIVLWIRR.DNTEIPAPIDSWLPGAHEKISQQQLLYATN.FGED
Retrocopy TQSWKTKSFILKYILLPVGSIVTLVAFIVLWIRRQDNTEIPAPIDSWLPGAHEKISQQQLLYATNDFGED

Parental  NLIGKGSLGMVYKGVLSNGLTVAIKVFNLEFQGALRSFDSECEVMQGICHRNLIRIITCCSNLDFKALVL
          NLIGKGSLGMVYKGVLSNGLTVAIKVFNLEFQGALRSFDSECEVMQGICHRNLIRIITCCSNLDFKALVL
Retrocopy NLIGKGSLGMVYKGVLSNGLTVAIKVFNLEFQGALRSFDSECEVMQGICHRNLIRIITCCSNLDFKALVL

Parental  EYMPKGSLDKWLYSHNYFLDLFQRLNIMIDVASALEYLHHDCSSLVVHCDLKPSNVLLDNNMVAHVADFG
          EYMPKGSLDKWLYSHNYFLDLFQRLNIMIDVA.ALEYLHHDCSSLVVHCDLKPSNVLLDNNMVAHVADFG
Retrocopy EYMPKGSLDKWLYSHNYFLDLFQRLNIMIDVALALEYLHHDCSSLVVHCDLKPSNVLLDNNMVAHVADFG

Parental  IARLLTETESMQQTKTLGTIGYMAP
          IARLLTETESMQQTKTLGTIGYMAP
Retrocopy IARLLTETESMQQTKTLGTIGYMAP

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_44 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Vitis vinifera	VIT_10s0003g04830	2 retrocopies	retro_vvin_44 , retro_vvin_45,