RetrogeneDB ID: retro_opri_589

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_18372:50295..50779(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL3
• Ensembl ID: ENSOPRG00000000501
• Aliases: None
• Description: mitochondrial ribosomal protein L3 [Source:HGNC Symbol;Acc:10379]

Sequence

>retro_opri_589
AACATCCCGTTCGCTAAGCAGTTCGTGTCTGATGAAGCCCAGTTGGCCAGTAAGCTGTGCCCCTCAAAGAAGAACCCTGG
CCACTGCGTCCGTGGGAAGCAGGTTCTACCAGGGTTGGCCTGATCGCTTTGAAGCTGGGCGTGATGCCCTGATGGACCAA
GGATGGTCGCAGGCTTGTGGCGACACTTCTCCAGGTACAGGACTGTCATGTCCTAAAATACACTTCAAAGGAAAACCATA
ACAGGAAAATGGCGGCCCTAACTGTAGGAGGAAAACTATATCCCACCTCGGGAAACCTACCTCAACATTGGAGTTTTACC
AAGAACCTGGCTTGCCACCAAAGTAGAAAGTCAAAATCCTCCATGTCACAGATAATGCTATAATTAATCCAGGTAAGCCT
CTGTATGCTGCTCAGCTCTGCCCAGGACAATACGTGGACGCCACAGCCAAAACTATTGGTAAAGGTTTCCAAGGCATCAT
GAAG

Alignment

ORF - retro_opri_589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.71 %
• Parental protein coverage: 51.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVPFVKQLVSDEDKAQLASKLCP-LKDE-LSLHPWEPGSSRVGLIALKLGMMPLWTKDGRRHVATLLQVQ
          N.PF.KQ.VSDE..AQLASKLCP.LK.E...L.PWE.GS.RVGLIALKLG.MP.WTKDGRR.VATLLQVQ
Retrocopy NIPFAKQFVSDE--AQLASKLCP<LKEEPWPLRPWEAGSTRVGLIALKLGVMP*WTKDGRRLVATLLQVQ

Parental  DCHVLKYTSKENHNGKMAALTVGG-KTVSRFWKSPSILEFYRELGLPPKQKVKIFHVTDNAVIKPGTPLY
          DCHVLKYTSKENHN.KMAALTVGG.KT.S...K..S.LEFY.E.GLPPK.KVKI.HVTDNA.I.PG.PLY
Retrocopy DCHVLKYTSKENHNRKMAALTVGG<KTISHLGKPTSTLEFYQEPGLPPK*KVKILHVTDNAIINPGKPLY

Parental  AAHFRPGQYVDVTAKTIGKGFQGVMK
          AA...PGQYVD.TAKTIGKGFQG.MK
Retrocopy AAQLCPGQYVDATAKTIGKGFQGIMK

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_589 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021216	1 retrocopy	retro_cpor_324,
Dasypus novemcinctus	ENSDNOG00000014498	1 retrocopy	retro_dnov_178,
Homo sapiens	ENSG00000114686	1 retrocopy	retro_hsap_1236,
Gorilla gorilla	ENSGGOG00000011128	1 retrocopy	retro_ggor_969,
Microcebus murinus	ENSMICG00000009524	1 retrocopy	retro_mmur_1106,
Ochotona princeps	ENSOPRG00000000501	1 retrocopy	retro_opri_589 ,
Pan troglodytes	ENSPTRG00000015396	1 retrocopy	retro_ptro_850,
Sus scrofa	ENSSSCG00000011179	1 retrocopy	retro_sscr_126,