RetrogeneDB ID: retro_opri_63

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1635:45807..46368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX4
• Ensembl ID: ENSOPRG00000008347
• Aliases: None
• Description: glutathione peroxidase 4 [Source:HGNC Symbol;Acc:4556]

Sequence

>retro_opri_63
AAGCCAGCACTGCTGTGCAGGGCCCTAGGCCAATCCCGGCCTGGCGGGCATGTTGTGTGCATCCTGTGACAGACAGCTGG
CACTGAGCATGCTCCTGCACAAGTTCTCAGCCAAGCACATGACGGGTGCATGGTTTGCCTGGACAAGTATGGATCTGGGT
ATCAATCATCAACAATGTGACCTCTCAATGAGGCAAAACAAATACGAATAGTACTCACTCATCAACTTTCACACACGATA
GGCTGAGTGTGGTTTGCACATCCTGGCCTTACCCTACAATCAGTTTGGGAAGCAGTAGCCAGGGAGTAACACCAAAATCA
AAGAGTTGGCTGCTAGCTATAATGTCACATTCAATATGTACAGCAAGATCTGCATGAACGTTGATGACACGCATTCTTTA
TGGAAGTGGATGAAAGTCCAGCTGAAGGTCAGGGGAATCCTGAGCAACACCATCAAGTGGATCTTCACCAAGTTCCTCAG
CAACAAGAATGCTGTGTGGTAGAGTGGTACAGCCCTATGGAGGAGTCCCTGGTGACACAGAAGGACTTACCTTGCTATCT
C

Alignment

ORF - retro_opri_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 94.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KPALLCGAL-AAPGLAGTMCASRD-DWRCARSMHEFSAKDI-DGRMVCLDKYRG-FVCIVTNVASQUGKT
          KPALLC.AL.A.PGLAG..CAS.D.........H.FSAK...DG.MVCLDKY....V.I..NV.SQ.GKT
Retrocopy KPALLCRAL>ANPGLAGMLCASCDRQLALSMLLHKFSAKHM<DGCMVCLDKYGS<WVSIINNVTSQ*GKT

Parental  EVNYTQ-LVDLHARYAECGLRILAFPCNQFGRQEPGSNAEIKEFAASYNVKFDMYSKICVNGDDAHPLWK
          ..N.T..L...H.R.AECGL.ILA.P.NQFG.Q.PGSN..IKE.AASYNV.F.MYSKIC.N.DD.H.LWK
Retrocopy NTNSTH<LINFHTR*AECGLHILALPYNQFGKQ*PGSNTKIKELAASYNVTFNMYSKICMNVDDTHSLWK

Parental  WMKVQPKGRGMLGNAIKWNFTKFLVDKNG-CVVKRYGPMEEPLVIEKDLPCYL
          WMKVQ.K.RG.L.N.IKW.FTKFL..KN..CVV..Y.PMEE.LV..KDLPCYL
Retrocopy WMKVQLKVRGILSNTIKWIFTKFLSNKNA<CVVEWYSPMEESLVTQKDLPCYL

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_63 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022744	1 retrocopy	retro_fcat_1113,
Monodelphis domestica	ENSMODG00000005486	1 retrocopy	retro_mdom_1363,
Mus musculus	ENSMUSG00000075706	2 retrocopies	retro_mmus_1595, retro_mmus_560,
Ochotona princeps	ENSOPRG00000008347	4 retrocopies	retro_opri_1144, retro_opri_63 , retro_opri_705, retro_opri_929,