RetrogeneDB ID: retro_opri_112

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2363:441495..441830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF4
• Ensembl ID: ENSOPRG00000004317
• Aliases: None
• Description: ring finger protein 4 [Source:HGNC Symbol;Acc:10067]

Sequence

>retro_opri_112
AGTCCTGACATGGCCCTGGAGGCAGAGCTAATAGAACTAGGGGAAAATGATGAAGTGGTTGACCTCACCTGCGAGTCCGT
TGAACCTGTAGTGATTGACCTAACTTGCCATGACTCTGTTGTGATCACTGAGCAATGGAGAAGGCCAAGGAGAAACACAA
GGTCACGCCAAACTCAAACTGGTAGCTGTGCGGTAAGCAGTGATGGTCAGTGGGTGAGCAACAGAGATGTGTATGTGGCT
CGCAGTGCCCATCACTATTCTTCTGGAAGAAGGAACTGCAAGTCACTTACAACCTGGCTATATCAGTGTCGAGTGTGCAT
GATGGGTACTCAGAA

Alignment

ORF - retro_opri_112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.1 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TPEIALEAEPIELVETAGDEIVDLTCESLEPVVVDLTHNDSVVVSR--RRPRRNARRLRQDHADSCVLSS
          .P..ALEAE.IEL.E...DE.VDLTCES.EPVV.DLT..DSVV.....RRPRRN.R..RQ....SC..SS
Retrocopy SPDMALEAELIELGEN--DEVVDLTCESVEPVVIDLTCHDSVVITEQWRRPRRNTRS-RQTQTGSCAVSS

Parental  DEEELARDRDVYVTTHTP-TSARTDGAAGLRSSGTVS-CPICM-DGYSE
          D.......RDVYV......T.....G.A.....G..S.C..CM.DGYSE
Retrocopy DGQWVS-NRDVYVARSAH>TILLEEGTASHLQPGYIS<CRVCM<DGYSE

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_112 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Dipodomys ordii	ENSDORG00000006675	2 retrocopies	retro_dord_347, retro_dord_411,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Echinops telfairi	ENSETEG00000001683	3 retrocopies	retro_etel_469, retro_etel_626, retro_etel_627,
Felis catus	ENSFCAG00000004051	1 retrocopy	retro_fcat_897,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Myotis lucifugus	ENSMLUG00000005969	1 retrocopy	retro_mluc_1640,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Ochotona princeps	ENSOPRG00000004317	3 retrocopies	retro_opri_112 , retro_opri_783, retro_opri_863,
Procavia capensis	ENSPCAG00000004528	1 retrocopy	retro_pcap_208,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Sus scrofa	ENSSSCG00000008690	1 retrocopy	retro_sscr_181,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,