RetrogeneDB ID: retro_vvin_154

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 5:23969507..23970011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0062g01190
• Aliases: None
• Description: None

Sequence

>retro_vvin_154
ATGTCTGGATCAGATCATTCCTCTGGTTTTGACCAGCTAAGGTTGATGGTCAAGAAGGTCTTGGCCAAGCCTCAACGTGA
GGGTGAGGGTGTTGTTGTTAGGAGGAGCATTGGAAAGAGTGAATTGAAAAAACCTGGATCCTTTTCTCATGTTGGATAAG
TTCACAGTCGCACCATTGCTGGTTTTCCGGATCATCCACACAGAGGCTTTGAGACTGTTACATACATGCTGCAGGGAGCT
TTCACTCATCAAGATTTTGTAGAGCATAAGGGCACAATCCGAACAGGAAATGTGCAGTGGATGACTGTAGGCAGAGGCAT
AATCCACTCTGAAATGCCCGTAAGTGAAGGAACCCAAAAGGGATTGCAGTTTTGGATCAATCTAACATCCAAAGAAAAAA
TGATTGAACCAAATTACCAAGAATTGCCAAGTGAAGACATCAAAAGAGCAGAGAAAGATGGCGTTAAAGTCTAGGTCACA
ACTGAGGAAGAGCAGCCCGCAAGG

Alignment

ORF - retro_vvin_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.12 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGSDHSSGFDQPRLVVKKVLAKPQREGEGAVVRRSIGRSELK-NLDPFLMLDEFAVAPP-AGFPDHPHR
          MSGSDHSSGFDQ.RL.VKKVLAKPQREGEG.VVRRSIG.SELK.NLDPFLMLD.F.VAP..AGFPDHPHR
Retrocopy MSGSDHSSGFDQLRLMVKKVLAKPQREGEGVVVRRSIGKSELK>NLDPFLMLDKFTVAPL<AGFPDHPHR

Parental  GFETVTYMLQGAFTHQDFAGHKGTIRTGDVQWMTAGRGIIHSEMPADEGTQKGLQLWINLASKDKMIEPN
          GFETVTYMLQGAFTHQDF..HKGTIRTG.VQWMT.GRGIIHSEMP..EGTQKGLQ.WINL.SK.KMIEPN
Retrocopy GFETVTYMLQGAFTHQDFVEHKGTIRTGNVQWMTVGRGIIHSEMPVSEGTQKGLQFWINLTSKEKMIEPN

Parental  YQELPSEDIKRAEKDGVEVRVIAGESMGVR
          YQELPSEDIKRAEKDGV.V.V...E....R
Retrocopy YQELPSEDIKRAEKDGVKV*VTTEEEQPAR

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_154 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_05s0062g01190	1 retrocopy	retro_vvin_154 ,