RetrogeneDB ID: retro_opri_170

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3190:23844..24246(-)
• Located in intron of: ENSOPRG00000015304

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGCT
• Ensembl ID: ENSOPRG00000005329
• Aliases: None
• Description: gamma-glutamylcyclotransferase [Source:HGNC Symbol;Acc:21705]

Sequence

>retro_opri_170
ATGGCAGACTTGAGCTGCAATGAAGACTTGGGCCAGGCGGAGGACATTTTCTGTACTTTGCATAAGGCAGCAACCTGCTA
ACTGAAAAGAATCCACCTCCGAAACACTTCAACCAAGTTCTGCTGTGTAGCCCTCCTGCAGGATTTTACAACGGACTTCT
ACAATCTCCAAGGCAAAACAAGCCAGCAGTAGCAGGGAGGAGGAGCCACCATTTACCACAGTCCTGGTGATGAAGCGTGG
GAAGTCATATGGAAAATGGACAAAAGCAATCAAAGTTCTCTGGATGAGCAAGAACGGGTGGAAAGTGGAATCTACATTGT
GATAGAAGTTAAGGTGTCAACTCAAGACGGGAGAAAATTAACCTGTTCAAGTTACCTGATGACAAATTATGAGTGTTCCC
CC

Alignment

ORF - retro_opri_170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 71.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADSACEEDSGQGEDTF-LYFAYGSNLLTE-RIHLRNPSAKFCCVARLQDFTLDFGNFQGKTSQRWHGGI
          MAD..C.ED.GQ.ED.F.LYFA.GSNLLTE.RIHLRN.S.KFCCVA.LQDFT.DF.N.QGKTSQ...GG.
Retrocopy MADLSCNEDLGQAEDIF<LYFA*GSNLLTE>RIHLRNTSTKFCCVALLQDFTTDFYNLQGKTSQQ*QGGG

Parental  ATIYQSPGDEVWGVVWKMDKSNLSSLDEQEGVESGIYIVIEVKVSTQERKELTCRSYLMTNYESAP
          ATIY.SPGDE.W.V.WKMDKSN.SSLDEQE.VESGIYIVIEVKVSTQ....LTC.SYLMTNYE..P
Retrocopy ATIYHSPGDEAWEVIWKMDKSNQSSLDEQERVESGIYIVIEVKVSTQDGRKLTCSSYLMTNYECSP

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_170 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008757	1 retrocopy	retro_chof_467,
Callithrix jacchus	ENSCJAG00000008589	1 retrocopy	retro_cjac_1211,
Dasypus novemcinctus	ENSDNOG00000007242	1 retrocopy	retro_dnov_2324,
Mustela putorius furo	ENSMPUG00000005083	1 retrocopy	retro_mputfur_1157,
Otolemur garnettii	ENSOGAG00000013316	1 retrocopy	retro_ogar_2457,
Ochotona princeps	ENSOPRG00000005329	2 retrocopies	retro_opri_170 , retro_opri_505,