RetrogeneDB ID: retro_vvin_145

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 4:1894257..1894656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_01s0010g03370
• Aliases: None
• Description: None

Sequence

>retro_vvin_145
GCCGCTATAGTGAATTACTCCAGAGAGTCAGGCAATCCCACCAAGTGTTGCAAGGCCAAGGACTCAGATTTCAGAGTTCA
TTTCAAGAATACTAGGGAGACTGCTCATGTCATTAGGAAGTTGCCTTTGGCTAAGGCCAAAAGGTATTTGGATGATGTTC
TGGTCCACAAGCAAGCCATACATTTCACCCACTTCTGTAAAGGTGTTGGACAAATTGCTTAGACCAAGAACATGCATTCA
AATGGGCAAGGACGCTGGCCTGTCAAATCTACTAAATACATCATAGTTTTGCTTAAATACGCCGAGAGTGATGCTGATTT
GAAAGGTTTGGATGTTGATTCACTCTACATATCTCACATCCAAGCGAACCAAGCACAGAAACAAAGGCGCCGCACATAC

Alignment

ORF - retro_vvin_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.45 %
• Parental protein coverage: 65.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAMVKYSREPDNPTKSCKARGLDLRVHFKNTRETAHAIRKLPLAKAKRYLEDVLVHKQAIPFTRFCRGVG
          .A.V.YSRE..NPTK.CKA...D.RVHFKNTRETAH.IRKLPLAKAKRYL.DVLVHKQAI.FT.FC.GVG
Retrocopy AAIVNYSRESGNPTKCCKAKDSDFRVHFKNTRETAHVIRKLPLAKAKRYLDDVLVHKQAIHFTHFCKGVG

Parental  RTAQAKNRHSNGQGRWPVKSAKYILDLLKNAESNADLKGLDVDSLYISHIQVNQAQKQRRRTY
          ..A..KN.HSNGQGRWPVKS.KYI..LLK.AES.ADLKGLDVDSLYISHIQ.NQAQKQRRRTY
Retrocopy QIA*TKNMHSNGQGRWPVKSTKYIIVLLKYAESDADLKGLDVDSLYISHIQANQAQKQRRRTY

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_145 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Glycine max	GLYMA05G27940	1 retrocopy	retro_gmax_10,
Triticum aestivum	Traes_7BS_586D1E6FD	1 retrocopy	retro_taes_91,
Vitis vinifera	VIT_01s0010g03370	2 retrocopies	retro_vvin_145 , retro_vvin_18,