RetrogeneDB ID: retro_opri_1137

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7792:36222..37062(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSOPRG00000014606
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_opri_1137
GACTTGTTGAGCATTATCAAGGGTATGAAAGTTGAATTGAGCGCAGCAAATGTACAGACAACAAGGCCACTCGGCCAAAG
GCAGCCAAAAAGCGTGGAGGCCACGATCAGCAGGCCTCCACGGGCCGCCAACAAAGCCCGGAGGAAGAGAGCCCAAGCCC
CTGAGTCCTGAGTTGGTGGCAGCCACATCCGCTGTTGCAGATTCTCTTCCCTTTGATAAGCAGAAGATCAAATCAGACCT
GCTCAGGCAGCTCCCGCAGCATGAGGAGGACGCGTGGGCACAGAGAGATGGGCCGAGAGCGAAAATTAGTTTTGGTAACA
TAATATCAGATATGAAAGTTACCAGACCTGCTGCAGTTAGAGTTCGCCAAGACCACAGCACCAGATTCAATTTGACGAAG
AGTGTGACAGCTCGCCTGAGCAGTCTGCCGATCTCAGGAAAGTTGTTAGGAGAGAGTTACTCAAAGGGAAGAGACTTAAT
ATTTTTGACATAGAGACATTTACTGAAGACGCACCTAAAACAGAAACGCCGCCTTAGCTCTGGGATATTGAATTTGCTAA
GCAGTTGGCTGCAGTCAGTGCACAGCCCTTTCAGAATGGCTTTGAGGAGATGATCCAGTGGACCAAGGAGGGGAAATTGT
GGGAGTTTCCGATTAACAACAAAGCAGGTTTTGATGATGATGGTTCAGAATTTCATGAACACATTTTCCTGGATCAACAC
CTGGAGGGTTTTCCAAAACAAGAACCAATCCGCCACTTCATGGAGCTGGTGACTTGTGGCCTTTCCTGAAATCCATATCT
CAGTGTGAGACAGAAGGTTGAGCACATAGAATGGTTTAGA

Alignment

ORF - retro_opri_1137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.78 %
• Parental protein coverage: 72.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLLSIIKGMKVELSAANVQTTRPPGQRLPKSVEATIGRPPR--DEARRKRA-KPLSPELVAAASAVADSL
          DLLSIIKGMKVELSAANVQTTRP.GQR.PKSVEATI.RPPR....ARRKRA.KPLSPELVAA.SAVADSL
Retrocopy DLLSIIKGMKVELSAANVQTTRPLGQRQPKSVEATISRPPRAANKARRKRA>KPLSPELVAATSAVADSL

Parental  PFDKQKTKSDLLRQLRQHEEDARAQRDGPRPKISFGNIISDMKVTRPAAVRVR-PRPEHQIQFDEESDSS
          PFDKQK.KSDLLRQL.QHEEDA.AQRDGPR.KISFGNIISDMKVTRPAAVRVR.PRP.HQIQFDEE.DSS
Retrocopy PFDKQKIKSDLLRQLPQHEEDAWAQRDGPRAKISFGNIISDMKVTRPAAVRVR<PRPQHQIQFDEECDSS

Parental  PEHSADLRK--RRDLFKGKRLNIFDIETFTEEAPKTETPPSLWDIEFAKQLAAVSAQPFQNGFEEMIQWT
          PE.SADLRK..RR.L.KGKRLNIFDIETFTE.APKTETPP.LWDIEFAKQLAAVSAQPFQNGFEEMIQWT
Retrocopy PEQSADLRKVVRRELLKGKRLNIFDIETFTEDAPKTETPP*LWDIEFAKQLAAVSAQPFQNGFEEMIQWT

Parental  KEGKLWEFPINNEAGFDDDGSEFHEHIFLDQHLEGFPKQGPIRHFMELVTCGLSRNPYLSVRQKVEHIEW
          KEGKLWEFPINN.AGFDDDGSEFHEHIFLDQHLEGFPKQ.PIRHFMELVTCGLS.NPYLSVRQKVEHIEW
Retrocopy KEGKLWEFPINNKAGFDDDGSEFHEHIFLDQHLEGFPKQEPIRHFMELVTCGLS*NPYLSVRQKVEHIEW

Parental  FR
          FR
Retrocopy FR

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_1137 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137 ,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,