RetrogeneDB ID: retro_opri_1182

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_897:293094..293376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM7
• Ensembl ID: ENSOPRG00000015568
• Aliases: None
• Description: LYR motif containing 7 [Source:HGNC Symbol;Acc:28072]

Sequence

>retro_opri_1182
GGTCAGGTGGCGAAGGTTTTGCAGTTCTTCAAAACATCGCACAGGACCAGATAACAAGTTTTTAAAAATGATGCCAGAGC
ATTAGAAGCAGCCAGAATAAAAATAAATGAAGAATTCAAAAGTAATAAAAGTGAGACTTCTCCTGAGAAAATAGAGGAGC
TAATGAAAATAGGTTCCGATGTTGAACTGCTACTGAGAACATCTGTTATACAAGGTATCCACACAGACCACAATACACTG
AAATTGGTCCCTAGGAAAGACCTTCTTTTAGAAAATATGCCA

Alignment

ORF - retro_opri_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 90.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQAAKVLQLFKTLHRTRQQVFKNDARALEAARIKINEEFKSNKSETSPKKIEELIKIGSDVELLLRTSVI
          GQ.AKVLQ.FKT.HRTR.QVFKNDARALEAARIKINEEFKSNKSETSP.KIEEL.KIGSDVELLLRTSVI
Retrocopy GQVAKVLQFFKTSHRTR*QVFKNDARALEAARIKINEEFKSNKSETSPEKIEELMKIGSDVELLLRTSVI

Parental  QGIHTDHNTLKLVPRKDLLLENMP
          QGIHTDHNTLKLVPRKDLLLENMP
Retrocopy QGIHTDHNTLKLVPRKDLLLENMP

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_1182 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017776	1 retrocopy	retro_amel_1472,
Canis familiaris	ENSCAFG00000000736	1 retrocopy	retro_cfam_1279,
Choloepus hoffmanni	ENSCHOG00000006766	6 retrocopies	retro_chof_1440, retro_chof_2015, retro_chof_2366, retro_chof_2681, retro_chof_488, retro_chof_688,
Echinops telfairi	ENSETEG00000010130	1 retrocopy	retro_etel_1126,
Oryctolagus cuniculus	ENSOCUG00000000166	1 retrocopy	retro_ocun_1740,
Ochotona princeps	ENSOPRG00000015568	4 retrocopies	retro_opri_1182 , retro_opri_212, retro_opri_361, retro_opri_611,
Rattus norvegicus	ENSRNOG00000045961	1 retrocopy	retro_rnor_552,