RetrogeneDB ID: retro_vvin_9

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 3:18943191..18943821(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_03s0017g02200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_03s0017g02260
• Aliases: None
• Description: None

Sequence

>retro_vvin_9
ATGGGGAAGCTTGGTCTGGCTACCTGTTTGCTCATCCTTCTCAACTTGGCTACACTCCTCACTTCTCTTGCTCGTCCCTA
CCCCCCATACCCAACTCCTCCTAAACCAGCCAATAAAACGCACCCCCTTCTGACCCTTCCAGATAAACATCCTCCATACG
TCAAGCCAGCGCATACACCTAAGCCACCCAAGCCTCCGGTGGTCAAGCCACCCAAGCCTCCGGTGGTCAAACCACCCTAC
GTGCCTAAGCCTCCGGTTGTCAAGTCACCAGTGATTCCAAAGCCACCCCCAGTCGAGACACCATGCCCTCCTCCCCCACC
GCCACCACCACTGTACCCACCTCCGGCCCAGGTGACGCCCCCGCCACAAAAGACATGCCCCATTGACACTCTGAAGCTGG
GTGCATGTGTGGATTTGTTGGGAGGGCTTGTGCATGTTGGGATAGGAAGTAGTGCTAAGGACACATGCTGTCCGGTGCTG
CAAGGGCTTGTGGACTCGGACTCTGCCCTGTGTCTTTGCACCACCATCAAGGCCAAGCTTCTTAATGTCAATATCATCAT
ACCCATTGCTCTTCAAGTCCTTGTTGACTGTGGCAAGACTCCACCTCCAGGATTCCAATGCCCTGCCTAA

Alignment

ORF - retro_vvin_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.31 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHPLPPLPPKHPPHVKPPHTPMPPKPPVVKPPYVPKPPVVQPP----PPPVVHPPPPPTPCPP--PPPPK
          KHP.P...P.H.P....P....PPKPPVVKPPYVPKPPVV..P....PPPV..P.PPP.P.PP..PPP..
Retrocopy KHP-PYVKPAHTPKPPKPPVVKPPKPPVVKPPYVPKPPVVKSPVIPKPPPVETPCPPPPPPPPLYPPPAQ

Parental  GRPPPQQTCPIDTLKLGACVDLLGGLVHIGIGSSAKDTCCPVLQGLVDLDAAVCLCTAIKVKLLNVNIII
          ..PPPQ.TCPIDTLKLGACVDLLGGLVH.GIGSSAKDTCCPVLQGLVD.D.A.CLCT.IK.KLLNVNIII
Retrocopy VTPPPQKTCPIDTLKLGACVDLLGGLVHVGIGSSAKDTCCPVLQGLVDSDSALCLCTTIKAKLLNVNIII

Parental  PIALQVLVGCGKTPPSGFQCPA
          PIALQVLV.CGKTPP.GFQCPA
Retrocopy PIALQVLVDCGKTPPPGFQCPA

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_9 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_03s0017g02260	1 retrocopy	retro_vvin_9 ,