RetrogeneDB ID: retro_opri_881

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4041:58385..58702(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC24
• Ensembl ID: ENSOPRG00000001638
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 24 [Source:HGNC Symbol;Acc:26979]

Sequence

>retro_opri_881
ATAATGCCATCTGAACATATGCCAAGGAAGGACAAGTATAGCTTTCTGGGGGTAGACCCCTCTAAAATCATGTCAGATCT
AAGACCCAAACATCAAAAGCTTATATTATAGTATTACCCAGATAAACAGAGTACAGATATTCCAGTAGGAACAATGCAAA
AATATTTACAGAAGTTCATTGAAGTTGATCAGGCACAGAAAGTTCTAGGGAAGGAACAGCCAAAGACAGAGTATGACCTG
CAATGCCCGTGCAGATGATCTAAGAAATATGGGGCCAGTAGGTGCCCAAGTCTTGGAATGAAATGTCTTGGAAAGAA

Alignment

ORF - retro_opri_881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMASEQMPRKDWYSILGADPSENVSDLRQKYQKLVLKYHPDKQNTDVPAGTVEECLQKFIEVDQAWKVLG
          .M.SE.MPRKD.YS.LG.DPS...SDLR.K.QKL.L.Y.PDKQ.TD.P.GT....LQKFIEVDQA.KVLG
Retrocopy IMPSEHMPRKDKYSFLGVDPSKIMSDLRPKHQKLIL*YYPDKQSTDIPVGTMQKYLQKFIEVDQAQKVLG

Parental  NEETKTEYDLQ-RCEDDLRNMGPVDAQVYLE-EMSWNE
          .E..KTEYDLQ....DDLRNMGPV.AQV.LE.EMSW.E
Retrocopy KEQPKTEYDLQ>ARADDLRNMGPVGAQV-LE>EMSWKE

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_881 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013512	1 retrocopy	retro_dnov_2247,
Dipodomys ordii	ENSDORG00000000248	3 retrocopies	retro_dord_221, retro_dord_395, retro_dord_77,
Echinops telfairi	ENSETEG00000003054	1 retrocopy	retro_etel_161,
Microcebus murinus	ENSMICG00000007553	3 retrocopies	retro_mmur_1052, retro_mmur_1150, retro_mmur_973,
Macaca mulatta	ENSMMUG00000006845	1 retrocopy	retro_mmul_2112,
Nomascus leucogenys	ENSNLEG00000017878	1 retrocopy	retro_nleu_3029,
Otolemur garnettii	ENSOGAG00000007848	1 retrocopy	retro_ogar_1542,
Ochotona princeps	ENSOPRG00000001638	1 retrocopy	retro_opri_881 ,
Pongo abelii	ENSPPYG00000003390	2 retrocopies	retro_pabe_2783, retro_pabe_2788,
Pan troglodytes	ENSPTRG00000003471	1 retrocopy	retro_ptro_2301,
Tarsius syrichta	ENSTSYG00000009243	1 retrocopy	retro_tsyr_623,