RetrogeneDB ID: retro_opri_299

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4833:296220..296846(-)
• Located in intron of: ENSOPRG00000010504

Retrocopy information

• Ensembl ID: ENSOPRG00000010541
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSOPRG00000007883
• Aliases: None
• Description: RAB5B, member RAS oncogene family [Source:HGNC Symbol;Acc:9784]

Sequence

>retro_opri_299
GCGCGACCCAATGGACCAGCCGCCGGAAACAAGATCTGTCAGTTTAAGCTGGTCCTGCTGGGGGGGTCTGCAGTGGGCAA
GTCCAGCCTTGTCCTCTGCTTCGTCAAAGGGCAATTTCACGAGTACCAAGAGAGCACAGTTGGAGCGGCCTTTCTCACAC
AGACCTTCAGCTTGGACGACACCATGGTGAAGTTCGAGTTCTGGGACACAGCTGGCCAGCAGCGGTATCACAGCCTCCAC
CCCATGTACTTCCGGGGGCCCAGGCGGCCATTGTGCTATACGACATCACCAACACAGACACATTTGCACGGGCCGAGAAC
TGGGTGAAAGAGTTACAGAGACAGGCCAGCCCCAATATAGTCATTGCACTCGCAGGCAACAAGGCAGACCTGGACAGCAA
GAGCGCCGTGGAGTTCCAGGACGCACAAGCCTATGCAGACGAGAACAGTTTGCTGTTCATGGAGACCTCAGCAAAGACTG
CAATTAACGTGAATGAAATTTTCATGGCAACAGCCAAGCAGCTTCCCAAGAACGAGCCCCAGAATGCAGCTGGTGCTCCA
GGCCGGAACCGGGGTGCCGACCTCCAGGAGAACAACCCAGTGAGCCGGAGCCAGTGCTGCAGCAAC

Alignment

ORF - retro_opri_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 97.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVKFEIWDT
          ARPNG.....KICQFKLVLLG.SAVGKSSLVL.FVKGQFHEYQEST.GAAFLTQ...LDDT.VKFE.WDT
Retrocopy ARPNGPAAGNKICQFKLVLLGGSAVGKSSLVLCFVKGQFHEYQESTVGAAFLTQTFSLDDTMVKFEFWDT

Parental  AGQERYHSLAPMYYRG-AQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEY
          AGQ.RYHSL.PMY.RG.AQAAIV.YDITN..TFARA..WVKELQRQASP.IVIALAGNKADL..K..VE.
Retrocopy AGQQRYHSLHPMYFRG<AQAAIVLYDITNTDTFARAENWVKELQRQASPNIVIALAGNKADLDSKSAVEF

Parental  EEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKSQCCSN
          ..AQAYAD.NSLLFMETSAKTA.NVN..F.A.AK.LPK.EPQN..GA.GR.RG.DL.E......SQCCSN
Retrocopy QDAQAYADENSLLFMETSAKTAINVNEIFMATAKQLPKNEPQNAAGAPGRNRGADLQENNPVSRSQCCSN

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_299 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299 ,
Ochotona princeps	ENSOPRG00000011037	1 retrocopy	retro_opri_378,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,