RetrogeneDB ID: retro_opri_166

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3157:701379..701621(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSOPRG00000004366
• Aliases: None
• Description: ring finger protein 5, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10068]

Sequence

>retro_opri_166
GCAGCTGCCGAGAAGGATGGGGGTCCCTTAAGGGTCAAACCGCGAGCAAGACGCGGCAGGTGCGACCTTCAGATGTAACA
TACGGCTGGAGACTGCTTGGGAAGCCGTGGTCAGTGCATGTGGCCACCTGTACTGCTGGCCCTGCCTGCACCAGTGGCTG
GAGACCCGGCCGGAGCGGCAGCAGTGCCCGGTGTGTAAGGCTGAGCTCAGCAGAGTCAATTATCCCACTGTACGGGCGAG
GA

Alignment

ORF - retro_opri_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAEEEDGGPE-GPNRERGGAGATFECNICLETAREAVVSVCGHLYXXXXXXXWLEARPERQQCLVCKA-G
          AA.E.DGGP..G.NRE...AGATF.CNI.LETA.EAVVS.CGHLY.......WLE.RPERQQC.VCKA..
Retrocopy AAAEKDGGPL>GSNREQDAAGATFRCNIRLETAWEAVVSACGHLYCWPCLHQWLETRPERQQCPVCKA>S

Parental  SSESVVPLYGRG
          S.ES..PLYGRG
Retrocopy SAESIIPLYGRG

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_166 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166 , retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183,