RetrogeneDB ID: retro_opri_246

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_418:524771..525185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSOPRG00000004938
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]

Sequence

>retro_opri_246
GAGCTTAAGAAATACAGAGTGACCACAATAGTAAGAGTGTGCCAAGCGACTTACGACACTGCTCTTGTGGAGAAGGAGGG
CATCCAGGTTGTGGACTGGCCTTTTGACGATGGCTCGTCACCTTCCAAACAGATTGTTGATGATTGGGTAAGACTTGTAA
GCGTTAAATTCCGTGAAGAACCTGGTTGTTGTATCGCCGTTCACTGTGTTGCAGGTCTTGGCAGAACCCCAGTGCTGATT
GCCCTAGCGTTAATCGAAAGTGGAATGAAAAATGAAGATGCAGTGCAGTTGATTCGACAAAAGCGACGTGGAGCTTTTAA
CAGTAAGCAACTTTTGTATTTGGAGAAATACCATTCTAAAATGCGGCTGCGCTTTAAAGACTCCAATGGCCACAGAAACA
ACTGTTGCATTCAA

Alignment

ORF - retro_opri_246 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCV
          ELKKY.VTTIVRVC.ATYDT.LVEKEGI.V.DWPFDDG..PS.QIVDDW..LV..KFREEPGCCIAVHCV
Retrocopy ELKKYRVTTIVRVCQATYDTALVEKEGIQVVDWPFDDGSSPSKQIVDDWVRLVSVKFREEPGCCIAVHCV

Parental  AGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ
          AGLGR.PVL.ALALIE.GMK.EDAVQ.IRQKRRGAFNSKQLLYLEKY..KMRLRFKDSNGHRNNCCIQ
Retrocopy AGLGRTPVLIALALIESGMKNEDAVQLIRQKRRGAFNSKQLLYLEKYHSKMRLRFKDSNGHRNNCCIQ

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_246 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 17 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002490	3 retrocopies	retro_cfam_1832, retro_cfam_206, retro_cfam_593,
Cavia porcellus	ENSCPOG00000025759	5 retrocopies	retro_cpor_1137, retro_cpor_1233, retro_cpor_1392, retro_cpor_552, retro_cpor_58,
Dasypus novemcinctus	ENSDNOG00000018507	4 retrocopies	retro_dnov_1850, retro_dnov_278, retro_dnov_692, retro_dnov_996,
Equus caballus	ENSECAG00000022483	6 retrocopies	retro_ecab_10, retro_ecab_1075, retro_ecab_20, retro_ecab_425, retro_ecab_783, retro_ecab_869,
Echinops telfairi	ENSETEG00000008183	6 retrocopies	retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Latimeria chalumnae	ENSLACG00000007183	1 retrocopy	retro_lcha_90,
Loxodonta africana	ENSLAFG00000006572	8 retrocopies	retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus	ENSMLUG00000001162	1 retrocopy	retro_mluc_264,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Mustela putorius furo	ENSMPUG00000003118	1 retrocopy	retro_mputfur_17,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Ochotona princeps	ENSOPRG00000004938	4 retrocopies	retro_opri_246 , retro_opri_511, retro_opri_692, retro_opri_973,
Rattus norvegicus	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri	ENSTBEG00000009956	14 retrocopies	retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tursiops truncatus	ENSTTRG00000004129	6 retrocopies	retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,
Vicugna pacos	ENSVPAG00000004277	9 retrocopies	retro_vpac_167, retro_vpac_201, retro_vpac_275, retro_vpac_427, retro_vpac_476, retro_vpac_496, retro_vpac_535, retro_vpac_560, retro_vpac_583,