RetrogeneDB ID: retro_opri_358

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_816:65925..67319(-)
• Located in intron of: ENSOPRG00000016903

Retrocopy information

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

Parental gene information

• Parental gene symbol: WEE2
• Ensembl ID: ENSOPRG00000009103
• Aliases: None
• Description: WEE1 homolog 2 (S. pombe) [Source:HGNC Symbol;Acc:19684]

Sequence

>retro_opri_358
ATGGATGTGGAGAGCAGTAACAAACAGCTAAGTGGGAAATTAGGCTTGTTTCCTTGTGAACAGGGGACAGAGAACAAAGC
GCAGAGGGGAGCAGAAGAGGGTGAGGGAGTCCAGAGCCAGTCTCCGGAGAAGGAGGAGGTTCAGGACTCGGAGTCCTTCA
GGACACCCCTGAGGAGCGTAAGTGGGGTCCCTGGCACCTTTCAGAAAAGAGGCAAACCCATCCTAGGCCCAGTTCTGAGG
ACTCCAGTGTCAGCCTCTCCCACATGTCCTGAGACACCAGCTCTGCTGGAGAAAAGGAGCAAGATGCTGCATGCTGAGAG
CCCCTCCACTCTGAAAAACCTGCAGAGCCAGCCTCCAGCAATTTCTTCAACAGTGAAGCTCTCCTCCAGAGGCTCCAAGC
ATTTCAGGCACACGCCTGTTTCCCTCAGGGATGAGATGGCCTTGCTGGCTTTGGTCAATATTAATCCCTTCACTCCAGAG
TCCTTGAAAAAATTATTGCTTACACCCAATGGCAAGAGGAAAACCCGAGGAGATGTTGAGGAAACTGGTCCAGAAGAAGG
CAAATTAAAACAAGGGTTACCTGCCAAGAGATGTGTCATGAGAGAAACCAACATGGACACACACTATGAAAAGGAATTTT
TGGAGGTGGAAAAAATTGGAGTCGGGTCATTTGGTACAGTCTACAAATGCATTAAGAGGTTGGATGGATGTGTCTATGCA
ATAAAGCGTGCTACCAAGCCATCCACAGCATCTTCCAATGAAATTCAGATTTGCGAGAAGTCTATGCCCATGCAGTGCTA
GGCCATCACCCCCATGTAGTGCGTTACTACTCTGCCTGGTCAGAAGATGACTACATGATCATTCAGAATGAATACTGCAA
TGGTGGGAGTTTGCAAGCCGTTATATCTGAAAATACTAAGTCTGGTGATCATTTCCAAGAGCCCACACTCAGAGACATCC
TTCTGCAGATTTCCGTGGGAATTAAATACATCCACAACTCGGGGGTGGTGCACCTGGACATCAAACCTAGCAATATCTTC
ATTTGTCATAAGGTGCAAAGCGATTTTACTGACGTGCCAGAAGAGATTGAAAATGAAGCTGATTGGTTCATCTCTGCCAG
TGTGATATATAAAATTGGTGACCTGGGCCACGTATCATCCATAAGTGATCCCAGTGTAGAAGAAGGAGATATTCGCTTCC
TGGCTAATGAGGTTTTGCAAGAAGATTATCGACATCTTCCCAAGGCAGACATATTTGCCTTGGGCTTAACAATAGCGGTG
GCTGCGGGAGCCGGGGCGTTACCAGCCAACGGGGAGGCGTGGCATCACATCCGCAAGGGTAACCTTCCAGAAATTCCCCA
GAAACTCTCGGAAGACTTTCAAGATCTGCTCAAG

Alignment

ORF - retro_opri_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.85 %
• Parental protein coverage: 81.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSEW--TPLRNVSGVPGTFQKR
          MDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSE...TPLR.VSGVPGTFQKR
Retrocopy MDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSESFRTPLRSVSGVPGTFQKR

Parental  GKPILAPVLRTPVSASPTCPETPALLEKRSKMLHAESPSTPKNLQSQPPAISSTVKLSSRGSKHFRHTPV
          GKPIL.PVLRTPVSASPTCPETPALLEKRSKMLHAESPST.KNLQSQPPAISSTVKLSSRGSKHFRHTPV
Retrocopy GKPILGPVLRTPVSASPTCPETPALLEKRSKMLHAESPSTLKNLQSQPPAISSTVKLSSRGSKHFRHTPV

Parental  SLRDEMASLALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDTRYE
          SLRDEMA.LALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDT.YE
Retrocopy SLRDEMALLALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDTHYE

Parental  KEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE-NSDLREVYAHAVLGHHPHVVRYYSA
          KEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE.NSDLREVYAHAVLGHHPHVVRYYSA
Retrocopy KEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE<NSDLREVYAHAVLGHHPHVVRYYSA

Parental  WSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVGLKYIHNSGVVHLDIKPSNIFIC
          WSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVG.KYIHNSGVVHLDIKPSNIFIC
Retrocopy WSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVGIKYIHNSGVVHLDIKPSNIFIC

Parental  HKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF
          HKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF
Retrocopy HKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF

Parental  ALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK
          ALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK
Retrocopy ALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK

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_358 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004658	1 retrocopy	retro_btau_932,
Callithrix jacchus	ENSCJAG00000013627	1 retrocopy	retro_cjac_936,
Dipodomys ordii	ENSDORG00000015156	1 retrocopy	retro_dord_559,
Gorilla gorilla	ENSGGOG00000009609	1 retrocopy	retro_ggor_705,
Ochotona princeps	ENSOPRG00000009103	2 retrocopies	retro_opri_358 , retro_opri_841,
Pongo abelii	ENSPPYG00000018066	1 retrocopy	retro_pabe_684,
Pan troglodytes	ENSPTRG00000028383	1 retrocopy	retro_ptro_601,