RetrogeneDB ID: retro_opri_845

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3651:77410..78012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESD
• Ensembl ID: ENSOPRG00000011461
• Aliases: None
• Description: esterase D [Source:HGNC Symbol;Acc:3465]

Sequence

>retro_opri_845
TTAACTTGCACATAACAAAATTTCATAACAAAATTCGGTTTTCAGCAAGCTGCCTCTAAACATGGCCTTATTGTCATTGC
TCCAGATACCAGCCACAGTGGCTGCAATATTACAGATGACAGCTGGGACTTTGGCCCTGATGCTGGATTTTATGCAGGTG
CCCTTGAGAGTCTCTGGAATACCAACTACAGGACACATTCTTAAAAAACAGAAGAGCTTCCCCAGCTCACAAATGCCAAT
TTTCCAGTGTATCCCCAAAGCATGTCTATTGTTGGCCACTCCATGGGAGGTCATGGAGTTCTAATTTGTACTTTGAAAAA
GTCCTGGAAAATACAAATCTGTGTCAGCATTTGCTCCAATGTGCAACCCAGTACTCTGTATTTGGAGCAGAAAGCCTTTG
GTACCTTTTTTTGGGATCAGACCAAAATAAACAGAAGACTTACGATGCTGCCCATCTTGTGAAATACTATACAGGTCCTC
AGTTGCACATACTAATTGATCAAGGAAAAGCTGATGAGTTTTACAACGAGTTACACTCCGAGAACTTCATAGCTGCCTAT
GTGGAGAGGAAAATCCTTGTTGTTTTTAAATCACAAGAGGGA

Alignment

ORF - retro_opri_845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTCTEQNFITKSGFQQAASEHGLIVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVDATEDPWKTNYRMYSY
          LTCT.QNFITK.GFQQAAS.HGLIVIAPDTS..GCNI...DDSWDFG..AGFY..A.E..W.TNYR..S.
Retrocopy LTCT*QNFITKFGFQQAASKHGLIVIAPDTSHSGCNIT--DDSWDFGPDAGFYAGALESLWNTNYRTHS*

Parental  VTKELPQLVNANFPVDPQRTSIFGHSMGGHGALICTL-KNPGKYKSVSAFAPICNPVLCVWSKKAFA-AF
          .T.ELPQL.NANFPV.PQ..SI.GHSMGGHG.LICTL.K.PGKYKSVSAFAP.CNPVLC.WS.K.....F
Retrocopy KTEELPQLTNANFPVYPQSMSIVGHSMGGHGVLICTL>KSPGKYKSVSAFAPMCNPVLCIWSRKPLV>LF

Parental  LGPDQNKWQAYDATHLVKSYTGPQLDILIDQGKADEFYNELHPENFIAACTEKKIPVVFRSQEG
          LG.DQNK...YDA.HLVK.YTGPQL.ILIDQGKADEFYNELH.ENFIAA..E.KI.VVF.SQEG
Retrocopy LGSDQNKQKTYDAAHLVKYYTGPQLHILIDQGKADEFYNELHSENFIAAYVERKILVVFKSQEG

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_845 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 22 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013377	2 retrocopies	retro_amel_1085, retro_amel_1803,
Bos taurus	ENSBTAG00000003415	1 retrocopy	retro_btau_908,
Canis familiaris	ENSCAFG00000004473	2 retrocopies	retro_cfam_1381, retro_cfam_1762,
Callithrix jacchus	ENSCJAG00000009380	2 retrocopies	retro_cjac_24, retro_cjac_257,
Cavia porcellus	ENSCPOG00000011089	3 retrocopies	retro_cpor_1253, retro_cpor_1396, retro_cpor_568,
Dasypus novemcinctus	ENSDNOG00000017553	2 retrocopies	retro_dnov_2502, retro_dnov_96,
Equus caballus	ENSECAG00000024350	1 retrocopy	retro_ecab_808,
Felis catus	ENSFCAG00000026826	2 retrocopies	retro_fcat_1641, retro_fcat_812,
Loxodonta africana	ENSLAFG00000006901	1 retrocopy	retro_lafr_843,
Macaca mulatta	ENSMMUG00000004209	1 retrocopy	retro_mmul_1013,
Monodelphis domestica	ENSMODG00000011290	2 retrocopies	retro_mdom_1607, retro_mdom_1608,
Mustela putorius furo	ENSMPUG00000001494	2 retrocopies	retro_mputfur_1339, retro_mputfur_543,
Mus musculus	ENSMUSG00000021996	9 retrocopies	retro_mmus_1159, retro_mmus_1160, retro_mmus_1161, retro_mmus_1162, retro_mmus_1163, retro_mmus_1166, retro_mmus_1168, retro_mmus_1236, retro_mmus_1237,
Oryctolagus cuniculus	ENSOCUG00000009968	1 retrocopy	retro_ocun_709,
Otolemur garnettii	ENSOGAG00000010048	1 retrocopy	retro_ogar_162,
Ochotona princeps	ENSOPRG00000011461	2 retrocopies	retro_opri_230, retro_opri_845 ,
Procavia capensis	ENSPCAG00000004402	1 retrocopy	retro_pcap_354,
Pteropus vampyrus	ENSPVAG00000009910	3 retrocopies	retro_pvam_1309, retro_pvam_299, retro_pvam_87,
Rattus norvegicus	ENSRNOG00000009512	2 retrocopies	retro_rnor_1053, retro_rnor_1593,
Sarcophilus harrisii	ENSSHAG00000009581	3 retrocopies	retro_shar_307, retro_shar_337, retro_shar_570,
Ictidomys tridecemlineatus	ENSSTOG00000002854	2 retrocopies	retro_itri_182, retro_itri_639,
Tupaia belangeri	ENSTBEG00000005120	7 retrocopies	retro_tbel_1621, retro_tbel_1776, retro_tbel_2, retro_tbel_296, retro_tbel_3059, retro_tbel_3072, retro_tbel_3698,