RetrogeneDB ID: retro_vvin_52

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 11:8754812..8755199(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0049g00210
• Aliases: None
• Description: None

Sequence

>retro_vvin_52
AAAGAGAGGCGCGATTCAAAAGCTTTTCACCAGTCGAGCTGCGTCCATACATCAATGGCGTTCATTTCTTTCGTTGGGTG
AGTTCTTTTTGCTTCCGTCTTCTTTATTTTCGCTTGGCAAGAGTTTGATGAATCTGGTGTTGATGGTGGGCCTATAGCAG
AGTCGTTGGTCCCAAAGTTAAATGTTTTCTCTAAACATATGTCAACTAACGTTGGGGTCCAAGTGTCAGAAGTAGAAATT
AAAGATTTAGTGGCTGCATCTATAGTTTTGAAAGGCCTTGGAAGCCTTCTTTTTATCTTTGGCAGTTCTCTTGGAGCGCA
TCTCTCACTTCTTCATCAGGCAATTGTCATTCCTATCTTGTATGACTTTTACAACTATGATGTTGAC

Alignment

ORF - retro_vvin_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 56.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQRRDSKAFHQLSCVRTSMAFVSFVGRVLFASVFILSAWQEFNEFGVDGGPAVESLAPKLDVFSKHVSAN
          ..RRDSKAFHQ.SCV.TSMAF.SFVG.VLFASVF...AWQEF.E.GVDGGP..ESL.PKL.VFSKH.S.N
Retrocopy KERRDSKAFHQSSCVHTSMAFISFVG*VLFASVFFIFAWQEFDESGVDGGPIAESLVPKLNVFSKHMSTN

Parental  VGVQVPEVEIKNLVAASIALKGLGGLLFIFGSSLGAHLLLLHQAIVIPILYDFYNYDVD
          VGVQV.EVEIK.LVAASI.LKGLG.LLFIFGSSLGAHL.LLHQAIVIPILYDFYNYDVD
Retrocopy VGVQVSEVEIKDLVAASIVLKGLGSLLFIFGSSLGAHLSLLHQAIVIPILYDFYNYDVD

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_52 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	AC149475.2_FG002	4 retrocopies	retro_zmay_33, retro_zmay_42, retro_zmay_61, retro_zmay_79,
Vitis vinifera	VIT_05s0049g00210	2 retrocopies	retro_vvin_165, retro_vvin_52 ,