RetrogeneDB ID: retro_opri_62

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1599:1233581..1233803(-)
• Located in intron of: ENSOPRG00000001114

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50A
• Ensembl ID: ENSOPRG00000001182
• Aliases: None
• Description: transmembrane protein 50A [Source:HGNC Symbol;Acc:30590]

Sequence

>retro_opri_62
AGTGGGGGTGGTCTGGGTCGAACAGGTGCCTGCATCTGGCGCTTCATTGGTTTCATGTTGACCTTTGGCTAGCTGATTGC
CTCCATGTAGATCTTCTTTGGAGGTTATGTGGCAAAAGAAATACCCGCACTGTACCCTGGGATCACTGTGTTTTGGCAGA
ACGCCTTCATCTTCTTTGGAGGGCTGGTTTTGGAGTTTGGCCGCACCGAAGACCTACGGCAG

Alignment

ORF - retro_opri_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 58.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEGCLGQTGARIWLFIGFMLAFGSLIASMWILFGGYVAKEKSVVYPGIAVFFQNAFIFFGGLVFKFGRTE
          S.G.LG.TGA.IW.FIGFML.FG.LIASM.I.FGGYVAKE....YPGI.VF.QNAFIFFGGLV..FGRTE
Retrocopy SGGGLGRTGACIWRFIGFMLTFG*LIASM*IFFGGYVAKEIPALYPGITVFWQNAFIFFGGLVLEFGRTE

Parental  DLWQ
          DL.Q
Retrocopy DLRQ

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_62 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62 ,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,