RetrogeneDB ID: retro_opri_540

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_162882:376..853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS11
• Ensembl ID: ENSOPRG00000008247
• Aliases: None
• Description: mitochondrial ribosomal protein S11 [Source:HGNC Symbol;Acc:14050]

Sequence

>retro_opri_540
GCCGGGGCCCGGGGACTGTGCGATGCGCCCCCGCCGGAGGCAGCGGAGCAGGCGGCCGTGTGGCGCGGCGGCTTCAGCAT
CTACCCCCCACTTCCGGGGCAGGAGAGCTCCCTGAGGTGGGCAGGAAAGAAATTTGAGGAGATCCCGATTGCACACATCA
AGGCATCCTATAACAACACACAGATCCAGGTCGTATCTGCCACCAACCAATCACTCGCCCGCACATCCTGTGGCACAGAG
GGGTTTCGGAATGCCAAGAAGGCCACCGGTGTCGCCGCACAGACGGCAGCCATAGCTGCAGCGGCAAAAGCCTCAGGGAA
GGGGGTGACACACGTCCGCGTGGTGGTGAAGGGCCTGGGGCCAGGACACCTGTCAGCCATCAAGGGGCCGACCGTGGGGG
GCCTGGAAGTGATTGCCATCGCAGATAATACCCCTATCCCACACAATGGCTGCCACCCCAACAAGGCCAGGAGGCTG

Alignment

ORF - retro_opri_540 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 96.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGYWALRSCPWPRVAGRVVA---GARIYPPLPGQESSLRWAGKKFEEIPIAHIKASYNNTQIQVVSATNQ
          AG...L...P.P..A........G..IYPPLPGQESSLRWAGKKFEEIPIAHIKASYNNTQIQVVSATNQ
Retrocopy AGARGLCDAPPPEAAEQAAVWRGGFSIYPPLPGQESSLRWAGKKFEEIPIAHIKASYNNTQIQVVSATNQ

Parental  SLARTSCGTEGFRNAKKATGVAAQTAAIAAAAKASGKGVTHVRVVVKGLGPGRLSAIKGLTMGGLEVISI
          SLARTSCGTEGFRNAKKATGVAAQTAAIAAAAKASGKGVTHVRVVVKGLGPG.LSAIKG.T.GGLEVI.I
Retrocopy SLARTSCGTEGFRNAKKATGVAAQTAAIAAAAKASGKGVTHVRVVVKGLGPGHLSAIKGPTVGGLEVIAI

Parental  TDNTPIPHNGCRPKKARRL
          .DNTPIPHNGC.P.KARRL
Retrocopy ADNTPIPHNGCHPNKARRL

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_540 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601, retro_cjac_2989,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540 ,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808, retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419,