RetrogeneDB ID: retro_opri_125

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2535:43204..43450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000002478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DBI
• Ensembl ID: ENSOPRG00000008363
• Aliases: None
• Description: diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) [Source:HGNC Symbol;Acc:2690]

Sequence

>retro_opri_125
AGCCAGGTGGAATTTGAGATGGCGTGCGCGGCCGTCAAGCAGCTCAAGAACCCTCTGAGCGACCAGGAGAAGCTGCTGCT
GTACAGCCTCTACAAACAGGCCACTCAGGGCGACTGCAACCTCCCTGTGCCTCCTGTCTCAGAGGTGAGAGCCAAGGCCA
AGTGGGAGGCGTGGAACAAGATCAAAGGCATGTCCAAGATGGACGCCATGAGGAACTATGTGGCCAAAGTGGATGAGCTG
AAGAAA

Alignment

ORF - retro_opri_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.44 %
• Parental protein coverage: 78.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEAEFEKAAEEVKNLKAKPSDPEMLFIYSHYKQATVGDVNTDRPGMLDLKGKAKWDAWNELKGTSKESAM
          ...EFE.A...VK.LK...SD.E.L..YS.YKQAT.GD.N...P.......KAKW.AWN..KG.SK..AM
Retrocopy SQVEFEMACAAVKQLKNPLSDQEKLLLYSLYKQATQGDCNLPVPPVSEVRAKAKWEAWNKIKGMSKMDAM

Parental  KAYVDKVEELKQ
          ..YV.KV.ELK.
Retrocopy RNYVAKVDELKK

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_125 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 27 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008509	3 retrocopies	retro_amel_1587, retro_amel_69, retro_amel_993,
Bos taurus	ENSBTAG00000009517	2 retrocopies	retro_btau_154, retro_btau_1718,
Canis familiaris	ENSCAFG00000004895	6 retrocopies	retro_cfam_1228, retro_cfam_134, retro_cfam_1452, retro_cfam_1599, retro_cfam_570, retro_cfam_857,
Callithrix jacchus	ENSCJAG00000021436	1 retrocopy	retro_cjac_954,
Cavia porcellus	ENSCPOG00000000415	2 retrocopies	retro_cpor_576, retro_cpor_59,
Equus caballus	ENSECAG00000018949	1 retrocopy	retro_ecab_14,
Erinaceus europaeus	ENSEEUG00000012115	2 retrocopies	retro_eeur_101, retro_eeur_33,
Echinops telfairi	ENSETEG00000000220	5 retrocopies	retro_etel_1131, retro_etel_1403, retro_etel_1761, retro_etel_754, retro_etel_849,
Homo sapiens	ENSG00000155368	3 retrocopies	retro_hsap_1619, retro_hsap_3345, retro_hsap_3617,
Gorilla gorilla	ENSGGOG00000010372	3 retrocopies	retro_ggor_1224, retro_ggor_1289, retro_ggor_2442,
Loxodonta africana	ENSLAFG00000005002	2 retrocopies	retro_lafr_280, retro_lafr_42,
Microcebus murinus	ENSMICG00000000294	2 retrocopies	retro_mmur_1233, retro_mmur_291,
Macaca mulatta	ENSMMUG00000011126	3 retrocopies	retro_mmul_168, retro_mmul_651, retro_mmul_757,
Monodelphis domestica	ENSMODG00000000393	1 retrocopy	retro_mdom_61,
Mustela putorius furo	ENSMPUG00000000945	2 retrocopies	retro_mputfur_170, retro_mputfur_438,
Mus musculus	ENSMUSG00000026385	2 retrocopies	retro_mmus_2307, retro_mmus_712,
Nomascus leucogenys	ENSNLEG00000010290	2 retrocopies	retro_nleu_1170, retro_nleu_807,
Oryctolagus cuniculus	ENSOCUG00000004566	1 retrocopy	retro_ocun_234,
Ochotona princeps	ENSOPRG00000008363	3 retrocopies	retro_opri_125 , retro_opri_594, retro_opri_794,
Pongo abelii	ENSPPYG00000012788	2 retrocopies	retro_pabe_2755, retro_pabe_2968,
Pan troglodytes	ENSPTRG00000012401	2 retrocopies	retro_ptro_2140, retro_ptro_2446,
Pteropus vampyrus	ENSPVAG00000014349	5 retrocopies	retro_pvam_1120, retro_pvam_1121, retro_pvam_168, retro_pvam_529, retro_pvam_85,
Rattus norvegicus	ENSRNOG00000046889	3 retrocopies	retro_rnor_1801, retro_rnor_2737, retro_rnor_879,
Sus scrofa	ENSSSCG00000023435	3 retrocopies	retro_sscr_167, retro_sscr_375, retro_sscr_41,
Ictidomys tridecemlineatus	ENSSTOG00000006759	1 retrocopy	retro_itri_1,
Tupaia belangeri	ENSTBEG00000002067	13 retrocopies	retro_tbel_1617, retro_tbel_2338, retro_tbel_2726, retro_tbel_273, retro_tbel_3096, retro_tbel_3097, retro_tbel_3305, retro_tbel_3392, retro_tbel_3454, retro_tbel_3602, retro_tbel_4015, retro_tbel_556, retro_tbel_579,
Tarsius syrichta	ENSTSYG00000002108	2 retrocopies	retro_tsyr_142, retro_tsyr_1654,