RetrogeneDB ID: retro_opri_1007

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5694:736..1054(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSOPRG00000015368
• Aliases: None
• Description: desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]

Sequence

>retro_opri_1007
TGGATGAACAAGTACAGCTCACTTACTGGAATTGGAGTTTTTAATGAATGAATGGAAGTTTTTGGCAAAGAATTTGCTTA
TGGTGGTCATCCTTACCCTTTTCTGGAATATTTGAAATTTTGCCAGGCAATGGTTCTAAACTAGGAGAATCATTTCAATT
TAAACAAGCTGCTGTTTTAAGAAGCACTGACTTCCTAGAAGATGATAAAGAAAAAAATTGTAGAGGAACTGGGAATAGAA
TAGAAAGGCAATGCTTATCATTTGATGCACAAAAACTGCAATCACTTCTCTTCAGCTTTATCAGGGCTCAAGGTCGGC

Alignment

ORF - retro_opri_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 58.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WMNEYTSSIGIGVFHSGIEVYGREFAYGGHPY-PFSGIFEISPGNASELGETFKFKEAVVLGSTDFLEDD
          WMN.Y.S..GIGVF....EV.G.EFAYGGHPY.PFSGIFEI.PGN.S.LGE.F.FK.A.VL.STDFLEDD
Retrocopy WMNKYSSLTGIGVFNE*MEVFGKEFAYGGHPY<PFSGIFEILPGNGSKLGESFQFKQAAVLRSTDFLEDD

Parental  IE-KIVEELGKEYKGNAYHLMHKNCNHFSSALSEILCG
          .E.KIVEELG.E.KGNAYHLMHKNCNHFSSALS....G
Retrocopy KE>KIVEELGIE*KGNAYHLMHKNCNHFSSALSGLKVG

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000016	1 retrocopy	retro_chof_2439,
Dasypus novemcinctus	ENSDNOG00000003484	3 retrocopies	retro_dnov_1042, retro_dnov_2533, retro_dnov_539,
Erinaceus europaeus	ENSEEUG00000009507	2 retrocopies	retro_eeur_394, retro_eeur_470,
Homo sapiens	ENSG00000121644	1 retrocopy	retro_hsap_2071,
Gorilla gorilla	ENSGGOG00000009797	1 retrocopy	retro_ggor_1493,
Nomascus leucogenys	ENSNLEG00000004019	1 retrocopy	retro_nleu_2734,
Ochotona princeps	ENSOPRG00000015368	2 retrocopies	retro_opri_1007 , retro_opri_963,
Pongo abelii	ENSPPYG00000000055	1 retrocopy	retro_pabe_1685,
Pan troglodytes	ENSPTRG00000002180	1 retrocopy	retro_ptro_1384,
Sus scrofa	ENSSSCG00000010876	1 retrocopy	retro_sscr_388,
Drosophila melanogaster	FBgn0033551	1 retrocopy	retro_dmel_30,