RetrogeneDB ID: retro_vvin_45

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 10:8575441..8577279(+)
• 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_45
CTTGAAGAATTATATCTTGGTTATAACAAATTGACAGGTGGAATTCCTAGAGAGATTGGGAATCTTTCAAATTTAAATAT
TTTGCACTTAGCGTCTAGTGGAATCAATGGCCCTATTCCTGCCGAAATTTTCAATATCTCTTCATTGCACAGGATTGATT
TCACTAATAATAGCCTTTCGGGGGGTCTTCCAATGGATATTTGTAAACATCTTCCTAATCTCCAAGGGCTCTATCTTTCT
CAGAATCATCTCAGTGGTCAACTTCCTACAACTCTATTTTTATGTGGAGAGCTCCTGTTACTGTCATTATCAATCAATAA
ATTCACGGGAAGCATACCAAGAGATATTGGCAACTTATCAAAGCTTGAAAAGATCTATCTAAGCACCAATAGCCTCATAG
GTTCCATTCCAACTTCATTTGGTAATTTGAAGGCCTTAAAATTCCTTCAGTTGGGGTCCAACAATCTTACAGGGACGATA
CCAGAAGATATTTTTAACATCTCTAAACTACAGACCCTTGCGTTGGCGCAAAATCACCTTTCAGGCGGTCTTCCATCAAG
TATTGGCACTTGGCTCCCAGATCTTGAAGGGCTTTTTATAGGAGGCAATGAATTCAGTGGAACAATTCCAGTGTCTATTT
CAAATATGTCAAAACTTATCCGGCTACACATATCGGACAACTATTTCACTGGTAATATGCCAAAAGATCTCAGTAACCTA
AGGAAGCTTGAAGTTCTCAACCTTGCAGGCAATCAATTGACTGATGAACACTTAACCTCTAAGGTTGGTTTTCTTACTTC
TTTGACAAATTGCAAATTTTTGAGAACATTGTGGATAGATTATAATCCTTTAAGAGGCACTCTACCAAATTCACTAGGGA
ATCTTTCTGTTGCTCTTGAAAGTTTTACAGCATCAGCCTGCCATTTCAGAGGAACCATTCCCACAGGAATTGGTAATTTG
ACCAATTTGATATGGCTGGACCTGGGAGCTAATGACTTAACAGGGTCGATTCCAACTACATTGGGACAGCTACAGAAGCT
CCAACGATTGTACATTGCTGGAAATAGAATACAAGGATCCATTCCAAATGATCTTTGCCATTTGAAGAACTTGGGATACT
TGCATTTGAGTTCTAACAAATTGTCTGGATCAATCCCAAGTTGTTTTGGAGATCTTCCTGCGCTACGAGAACTCTCTCTT
GACTCCAATGTGTTAGCTTTCAACATTCCTATGTCCTTTTGGAGCCTTAGAGATTTGTTGGTTCTTAGCTTGTCTTCAAA
TTTCTTGACTGGTAATCTACCTCCCGAAGTTGGAAACATGAAGTCCATTACAACATTGGACCTGTCAAAGAACCTTATTT
CAGGTTACATTCCAAGAAGGATGGAAGAACTACAAAATTTGGTTAATCTTTCCTTGTCCCAAAACAAACTACACGGCTCA
ATACCGTAGAATTTGGTGATTTTCTAAGCTTGGAATCCATGGATCTATCTCAGAACAATTTATCTAGAACCATTCCCAAG
TCATTGGAGGCCCTTATTTATCTCAAGCATCTAAATGTTTCTTTCAATAAACTACAAGGAGAAATTCCAAATGGAGGACC
TTTCGTAAATTTCACTGCTGAATCGTTCATGTTCAATGAAGCCTTATGTGGAGCACCTCATTTTCAAGTCATGGCATGTG
ATAAAAACAACCGCACTCAATCATGGAAGACAAAGTCATTCATCTTGAAATATATTCTATTACCAGTCGGATCAATAGTA
ACTTTAGTGGTTTTCATTGTTCTGTGGATACGTAGACGAGATAACATGGAAATACCAACTCCAATTGATTCATGGCTC

Alignment

ORF - retro_vvin_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.95 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKELNLSSNHLSGKVPTGLGQCIKLQGISLSCNDFTGSIPSGIGNLVELQSLSLQNNSLTEG-EISSFSH
          L.EL.L..N.L.G..P...G....L....L......G.IP..I.N...L......NNSL..G.......H
Retrocopy LEELYLGYNKLTGGIPREIGNLSNLNILHLASSGINGPIPAEIFNISSLHRIDFTNNSLSGGLPMDICKH

Parental  CRELRVLKLSINH--GQLPTTLFLCGELLLLSLSINKFTGSIPRDIGNLSKLEKIYLSTNSLIGSIPTSF
          ...L..L.LS.NH..GQLPTTLFLCGELLLLSLSINKFTGSIPRDIGNLSKLEKIYLSTNSLIGSIPTSF
Retrocopy LPNLQGLYLSQNHLSGQLPTTLFLCGELLLLSLSINKFTGSIPRDIGNLSKLEKIYLSTNSLIGSIPTSF

Parental  GNLKALKFLQLGSNNLTGTIPEDIFNISKLQTLALAQNHLSGGLPSSIGTWLPDLEGLFIGGNEFSGTIP
          GNLKALKFLQLGSNNLTGTIPEDIFNISKLQTLALAQNHLSGGLPSSIGTWLPDLEGLFIGGNEFSGTIP
Retrocopy GNLKALKFLQLGSNNLTGTIPEDIFNISKLQTLALAQNHLSGGLPSSIGTWLPDLEGLFIGGNEFSGTIP

Parental  VSISNMSKLIRLHISDNYFTGNVPKDLSNLRKLEVLNLAGNQLTDEHLTSEVGFLTSLTNCKFLRTLWID
          VSISNMSKLIRLHISDNYFTGN.PKDLSNLRKLEVLNLAGNQLTDEHLTS.VGFLTSLTNCKFLRTLWID
Retrocopy VSISNMSKLIRLHISDNYFTGNMPKDLSNLRKLEVLNLAGNQLTDEHLTSKVGFLTSLTNCKFLRTLWID

Parental  YNPLKGTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLGHLQKLQRL
          YNPL.GTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLG.LQKLQRL
Retrocopy YNPLRGTLPNSLGNLSVALESFTASACHFRGTIPTGIGNLTNLIWLDLGANDLTGSIPTTLGQLQKLQRL

Parental  YIAGNRIQGSIPNDLCHLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDLM
          YIAGNRIQGSIPNDLCHLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDL.
Retrocopy YIAGNRIQGSIPNDLCHLKNLGYLHLSSNKLSGSIPSCFGDLPALRELSLDSNVLAFNIPMSFWSLRDLL

Parental  VLSLSSNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRMGELQNLVNLCLSQNKLQGSIP-VEFGDLL
          VLSLSSNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRM.ELQNLVNL.LSQNKL.GSIP.VEFGD.L
Retrocopy VLSLSSNFLTGNLPPEVGNMKSITTLDLSKNLISGYIPRRMEELQNLVNLSLSQNKLHGSIP<VEFGDFL

Parental  SLESMDLSQNNLFGTIPKSLEALIYLKHLNVSFNKLQGEIPNGGPFVNFTAESFIFNEALCGAPHFQVIA
          SLESMDLSQNNL..TIPKSLEALIYLKHLNVSFNKLQGEIPNGGPFVNFTAESF.FNEALCGAPHFQV.A
Retrocopy SLESMDLSQNNLSRTIPKSLEALIYLKHLNVSFNKLQGEIPNGGPFVNFTAESFMFNEALCGAPHFQVMA

Parental  CDKNNRTQSWKTKSFILKYILLPVGSAVTLVAFIVLWIRRRDNTEIPAPIDSWL
          CDKNNRTQSWKTKSFILKYILLPVGS.VTLV.FIVLWIRRRDN.EIP.PIDSWL
Retrocopy CDKNNRTQSWKTKSFILKYILLPVGSIVTLVVFIVLWIRRRDNMEIPTPIDSWL

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_45 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 ,