RetrogeneDB ID: retro_itri_500

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393296.1:9178369..9178645(+)
• Located in intron of: ENSSTOG00000005115

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSSTOG00000011179
• Aliases: None
• Description: VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:22082]

Sequence

>retro_itri_500
GCCGCCGCCAATGCTGCCGAGCCCAAGTCTGAAGGCGTTCTTGCCATGACTTTTAAGATTTTTCTCCTTTTTGCAGGACT
TATGGTTAAAGTTCCTGTGGGGTTATATTTTTCCTGTAAATTACTTCTTTTCCAGAGCCTGATGTTAATGTCCCCTGAAG
ACAGCGCCTTCTATGCGACTATTGTCGCGGTGGTCGGGCTGCATGTGGTGCTGGCGATTTTTGTCTTCATAGTGTGGAAG
GAGGGTTTGCCTCAGTGGCGGGAAAACAAAAATGAA

Alignment

ORF - retro_itri_500 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AALNALQPPEFRSESSLASTLKTLLFFTALMITVPIGLYFTTKSYIFEGILGMSNRDSYFYAAIVAVVAV
          AA.NA..P....SE..LA.T.K..L.F..LM..VP.GLYF..K...F.....MS..DS.FYA.IVAVV..
Retrocopy AAANAAEP---KSEGVLAMTFKIFLLFAGLMVKVPVGLYFSCKLLLFQSLMLMSPEDSAFYATIVAVVGL

Parental  HVVLALFVYVAWNEGSRQWREGKQD
          HVVLA.FV...W.EG..QWRE.K..
Retrocopy HVVLAIFVFIVWKEGLPQWRENKNE

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_500 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_500 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500 ,