RetrogeneDB ID: retro_opri_855

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3759:139121..139538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP30
• Ensembl ID: ENSOPRG00000007367
• Aliases: None
• Description: ribonuclease P/MRP 30kDa subunit [Source:HGNC Symbol;Acc:17688]

Sequence

>retro_opri_855
GCAACTTCTTCCAGGGTTCGGCTGTGTGATATTGTTGCTGTTTTTCCAAAGACTGGAAAATGGTTTTCATGTGGCTTGCA
CACGTTTGGATTTGGTCAGCATCACTGTGACAGAAAAACTACCATTTTACTTCGAAAGAACCCCTATTAATATGGCCATT
GACCGAGGCCTGGGCTTTGAACTTATTGATAGCCCTGCTATCAAAGACTCCACAATAAGAAGGTACACAATTTCCAATGC
ACTCAATTTGATGCAGATCTGCAAAGGAAAGAATGTAATTATATCCAGTGCTGCCGAAAGGCCTCTAGAAATAAGAGGAC
CATATGACATAACATACTTAGGGTTGTTATTTTGGACTCTGAAAGTGATGGCAAGGCTGCTGTGTCCACCGACTGCCAAG
CAGTGCTTCCCCATGGA

Alignment

ORF - retro_opri_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATSSRVRLYDIVAVFPKTEKLF-HVACTHLDVDLVCITVTEKLPFYFKRPPINVAIDRGLGFELVYGPAI
          ATSSRVRL.DIVAVFPKT.K.F.HVACT.LD..LV.ITVTEKLPFYF.R.PIN.AIDRGLGFEL...PAI
Retrocopy ATSSRVRLCDIVAVFPKTGKWF>HVACTRLD--LVSITVTEKLPFYFERTPINMAIDRGLGFELIDSPAI

Parental  KDSTIRRYTISNALNLMQICKGKNVIISSAAERPLEIRGPYDIANLGLLFGL-SESDGKAAVSTNCRAVL
          KDSTIRRYTISNALNLMQICKGKNVIISSAAERPLEIRGPYDI..LGLLF...SESDGKAAVST.C.AVL
Retrocopy KDSTIRRYTISNALNLMQICKGKNVIISSAAERPLEIRGPYDITYLGLLFWT<SESDGKAAVSTDCQAVL

Parental  LHG
          .HG
Retrocopy PHG

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_855 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006863	2 retrocopies	retro_mdom_1388, retro_mdom_1798,
Ochotona princeps	ENSOPRG00000007367	1 retrocopy	retro_opri_855 ,
Tursiops truncatus	ENSTTRG00000014708	1 retrocopy	retro_ttru_1152,