RetrogeneDB ID: retro_opri_288

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4670:9747..10081(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSOPRG00000009370
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_opri_288
TTCCGAAACCCCTGGTGCAGCTCATGATGGTCAAGAACATGACGCCCGCACCCTTGCTGCACTTCTTCCTGGATTCTTGA
GAGCAGGTCCTGGTGGAACCCAAGAGCAAGACGGAAATCATGGCACACATCCGGAGGATCTTGGGGAAGAGTAAGGAAGC
CCTCAAGAAAGAGGAGCAGGAGAAAAAGCAGCTAACTTTCACCCAGCCAACTTTGGGCCCTGGAAACACTGCCTGCGAGA
GTGCGTCTGTGAGGTAGGACAGGTGCCCTTTCCAGGCCTGGTCACCCAGGGAGACGACGGGAAGTACAAAGCGGCTCTGA
AGACCAATGGCAGG

Alignment

ORF - retro_opri_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.39 %
• Parental protein coverage: 67.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YRNPW-VQIMMFKNMTPSPFLRFYLDSGEQVLVDVETKSNKEIMAHIRRILGKSEETLKKEEQEKKQLSH
          .RNPW.VQ.MM.KNMTP.P.L.F.LDS.EQVLV..E.KS..EIMAHIRRILGKS.E.LKKEEQEKKQL..
Retrocopy FRNPW<VQLMMVKNMTPAPLLHFFLDS*EQVLV--EPKSKTEIMAHIRRILGKSKEALKKEEQEKKQLTF

Parental  -PANFGPR-KYCLRECMCEVEGQVPCPGLVPLPKEMTGKYKAALKASAQ
          .....GP..K.CLREC.CEV.GQVP.PGLV.......GKYKAALK....
Retrocopy TQPTLGPG<KHCLRECVCEV-GQVPFPGLVTQGDD--GKYKAALKTNGR

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_288 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288 , retro_opri_690, retro_opri_951,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,