RetrogeneDB ID: retro_opri_302

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4916:32482..32911(-)
• Located in intron of: ENSOPRG00000010661

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000015394
• Aliases: None
• Description: None

Sequence

>retro_opri_302
GTTTGGGAACTTGTCCTGGACAATTGGAAATCAAATGATGAAAAACTTGAGGGCTTAACAGCCGAATTTGTGAATTTAGC
ATTTCTCAGTTTAATAAACATAGGCTTGATCTCAGTTTCAAATCTCTCCAAGCTACCTAAATTGAAAAAACTTGAGCCCA
GTGACAATAGAATCTTTGGAGGTCTCGACATGTTAGCAGAAACACTTCCAAACCTTACATATCTAAACTTGAGTGGAAAT
AAGCTGAAAGATAGTAGCGCCTTGGAGCCTTTGAAAAAGTTGTATTGTCTGAAAAGCCTAGATCTGTTTAACTGTGAGGT
CACTAACCTGAATGACTACCAAGAGAGCGTCTTCCGACTCCTGCCCCAGCTGACCTACCTAGACGGTTATGATCGAGAGG
ACCGGGAAGCTCCTGACTCGGATACTCAG

Alignment

ORF - retro_opri_302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 62.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKELVLDNCRSIEGKIEGLTDEFEELEFLSTINVGLTSVANLPKLNKLKKLELSDNRISGGLEVLAEKCP
          V.ELVLDN..S...K.EGLT.EF..L.FLS.IN.GL.SV.NL.KL.KLKKLE.SDNRI.GGL..LAE..P
Retrocopy VWELVLDNWKSNDEKLEGLTAEFVNLAFLSLINIGLISVSNLSKLPKLKKLEPSDNRIFGGLDMLAETLP

Parental  NLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFELLPQLTYLDGYDRDDKEASDS
          NLT.LNLSGNK.KD.S..EPLKKL..LKSLDLFNCEVTNLNDY.E.VF.LLPQLTYLDGYDR.D.EA.DS
Retrocopy NLTYLNLSGNKLKDSSALEPLKKLYCLKSLDLFNCEVTNLNDYQESVFRLLPQLTYLDGYDREDREAPDS

Parental  DAE
          D..
Retrocopy DTQ

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_302 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000010058	3 retrocopies	retro_opri_1223, retro_opri_52, retro_opri_774,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302 , retro_opri_563,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,