RetrogeneDB ID: retro_opri_22

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1046:320844..321066(-)
• Located in intron of: ENSOPRG00000011225

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB1
• Ensembl ID: ENSOPRG00000012731
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa [Source:HGNC Symbol;Acc:7695]

Sequence

>retro_opri_22
CTAGCTGCCCTTGGTTGTGGGGTCGCTGTTGGCACCAGGACCGGAGTCATGGCAAACTTACTTCACTTGGTGCGCGACCA
CTGGGTGCATCTGCTTGTCCCTGTGGGCTTTGTCTTCGGATGCTACCTGGACAGGAGGAGCGATGAAAAGCTCACAGCTT
TCCAAAACAAGAGCATGCTGTTTAAAAGGGAGTTGAGGCCTAATGAAGAAGTTACCTGGAAA

Alignment

ORF - retro_opri_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAALGGGVAVGTRAGAVMASLLHLVRDHWVHLLVPVGFVFGCYLDRRSDEKLTAFRNKSMLFKRELRPNE
          LAALG.GVAVGTR.G.VMA.LLHLVRDHWVHLLVPVGFVFGCYLDRRSDEKLTAF.NKSMLFKRELRPNE
Retrocopy LAALGCGVAVGTRTG-VMANLLHLVRDHWVHLLVPVGFVFGCYLDRRSDEKLTAFQNKSMLFKRELRPNE

Parental  EVTWK
          EVTWK
Retrocopy EVTWK

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_22 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014837	1 retrocopy	retro_amel_1060,
Callithrix jacchus	ENSCJAG00000018067	5 retrocopies	retro_cjac_1027, retro_cjac_1053, retro_cjac_1330, retro_cjac_2586, retro_cjac_3294,
Homo sapiens	ENSG00000183648	2 retrocopies	retro_hsap_2646, retro_hsap_311,
Macaca mulatta	ENSMMUG00000022428	2 retrocopies	retro_mmul_1520, retro_mmul_538,
Nomascus leucogenys	ENSNLEG00000017129	1 retrocopy	retro_nleu_652,
Ochotona princeps	ENSOPRG00000012731	2 retrocopies	retro_opri_22 , retro_opri_992,
Pongo abelii	ENSPPYG00000006076	1 retrocopy	retro_pabe_2325,
Pan troglodytes	ENSPTRG00000006649	2 retrocopies	retro_ptro_1782, retro_ptro_253,
Pteropus vampyrus	ENSPVAG00000015319	1 retrocopy	retro_pvam_642,
Tursiops truncatus	ENSTTRG00000008130	2 retrocopies	retro_ttru_1515, retro_ttru_830,
Vicugna pacos	ENSVPAG00000003502	2 retrocopies	retro_vpac_257, retro_vpac_39,