RetrogeneDB ID: retro_itri_1624

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393579.1:1498061..1498298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VHL
• Ensembl ID: ENSSTOG00000013959
• Aliases: None
• Description: von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12687]

Sequence

>retro_itri_1624
CACCAGACGGTGCTGCCGGGCAGGAACCTCAGCATCCACAGCTACCGAGATCACCTTTGGCTCTTCAGAGATGCAGGCAC
AGACGACGGGCTTCTGGTTAACCTAACTGAGCTCTTCGTGCCATCTCTCAACGTGGATGGACAGCCTATTTTTTTGCCAG
CATCACTCTGGCCATGTGTATACCCTGAAAGAGCCATGCCTGCAGGTTGTGCGAAGCCTAGTCAAGCCCGAGAACTC

Alignment

ORF - retro_itri_1624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.02 %
• Parental protein coverage: 50.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPTLPPGTGRRIHSYRGHLWLFRDAGTYDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVR
          ..T..PG....IHSYR.HLWLFRDAGT.DGLLVN.TELFVPSLNVDGQPIF....L......ER......
Retrocopy HQTVLPGRNLSIHSYRDHLWLFRDAGTDDGLLVNLTELFVPSLNVDGQPIFLPASLWPCVYPERAMPA--

Parental  SLVKPENYRRL
          ...KP...R.L
Retrocopy GCAKPSQAREL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1624 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1624 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010456	1 retrocopy	retro_ggor_1259,
Otolemur garnettii	ENSOGAG00000007587	1 retrocopy	retro_ogar_2307,
Pongo abelii	ENSPPYG00000013663	1 retrocopy	retro_pabe_275,
Ictidomys tridecemlineatus	ENSSTOG00000013959	1 retrocopy	retro_itri_1624 ,