RetrogeneDB ID: retro_vvin_175

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 8:9200197..9200848(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0038g03690
• Aliases: None
• Description: None

Sequence

>retro_vvin_175
ATGCACAATGAAAATTGAATCAGGGTGCTCACGTCTTTGGGAAACTCTTCATTACCAAAAGAGAGAGAATCTGTTATTAA
TGCCATTAAGGTTTTTGGCATTAAGAGACCACCATATGAGTGCTTAGCGAGTCTCCTTGAAGACCACTCTCGCAGAATTG
ATGCAACAACTGACCATTTTGTGTATGTTCATAGAAAATCTTGAGCAGTACTAAGAAAGAGCAACAGTTGCGACAACCGA
AGCAATAATGTTCATTGTCCACATATGGGGCAAGTTGGCCACAATGATGAGACAACCTAGTTGATGCACATGCTATCTAG
GAAACCTATTAATCCTCATCTTGGAAAGATTGGCAATAGTTTACCCTCAGCAAAAACCAATTATCCTCCTATTATTTCTG
TTATTTTTTTTTTTGATAATCCAAGGGGAATGAAAAGTTAGCATTGGGAAGAACATAATATTCAATTGCAGAGATTGTTG
AGGAAATTAGACCAATCAAATCAAGAGGATTATCTCCGGATGTTTTGCTTCTTGTCTTCCATTGAACTTAGCGGGCATGC
TGTAAAGTTGAAAATGAGATCAATTCAATTTACATTGGAGGAAGGTAAAGAGTTGCAGTGAGCTGGAGCTTTGAACATAT
TGGAAAAACTA

Alignment

ORF - retro_vvin_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQNENRSRVPTSLGNSSLPKERESVINAIEVSGIKRPPSECLASLPEDHSRRIDATTGHFVYVRRKSEAV
          M.NEN..RV.TSLGNSSLPKERESVINAI.V.GIKRPP.ECLASL.EDHSRRIDATT.HFVYV.RKS.AV
Retrocopy MHNEN*IRVLTSLGNSSLPKERESVINAIKVFGIKRPPYECLASLLEDHSRRIDATTDHFVYVHRKS*AV

Parental  LRKSNTCDNRSNNAHCPHMGQLGHNEETTQLMHTLSRKPTDPPLGKTGNRLPPAEANYPPITSAIPFLDN
          LRKSN.CDNRSNN.HCPHMGQ.GHN.ETT.LMH.LSRKP..P.LGK.GN.LP.A..NYPPI.S.....DN
Retrocopy LRKSNSCDNRSNNVHCPHMGQVGHNDETT*LMHMLSRKPINPHLGKIGNSLPSAKTNYPPIISVXXXXDN

Parental  PRGMKSQHWEERNLQLQRLLRKLDQSNQEDYLQMLRSLSSIELSRHAVKLERRSIQLSLEEGKELQRVGA
          PRGMKS.HWEE.N.QLQRLLRKLDQSNQEDYL.M...LSSIELS.HAVKL..RSIQ..LEEGKELQ..GA
Retrocopy PRGMKS*HWEEHNIQLQRLLRKLDQSNQEDYLRMFCFLSSIELSGHAVKLKMRSIQFTLEEGKELQ*AGA

Parental  LNILEKL
          LNILEKL
Retrocopy LNILEKL

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_175 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_03s0038g03690	1 retrocopy	retro_vvin_175 ,