RetrogeneDB ID: retro_opri_175

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3239:358727..359244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM192A
• Ensembl ID: ENSOPRG00000006909
• Aliases: None
• Description: family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]

Sequence

>retro_opri_175
GATGGAGGAGATGCTGGCAATCTTGTTATCAAAAAGAGTTTTGTGTCAGAGGCAGGACTAGACTAACGGCGCAAAAGGAC
GCAAGAAGAATGGGAGAAAATTCAAAGACAGGAAGATCTAGAGGAATGTCAGGGAGAAGCTTATGACCCCCGGTCTTTAT
GAAAGACTACAGGAGCAGAAAGACAGGAAGCAGCCGGAGTAGGAGGAGCAGTTCAAGTTTAAAACCATGGTAAGAGGCTT
AGATGAAGATGAGACCAACTTCCTTGATAAGGTTTCTCGGCAGCAAGAACTGATAGAAAAGCAGTGAAAAGAGGAAGAGC
TGAAAGAACTGAAGGAGTACAGAAGTAACCTCAGTAAGGCTGGACTGGCTTCAGAAAACAAGGAGGAAGTGGAGAAGAAG
CGGACTGTGAAACCCATACAAAGCAAGAACACGTTCTCCCAAGCGAAGCTGTTGGCAGGAGCTGTGAAGCCTGAGCTCAG
ACAGCGGCCACTGTGAAAACTGAAACCAGACCCAGAT

Alignment

ORF - retro_opri_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 68.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECP-EEAYDPRSLYERLQEQKDRKQQEYE
          DGGD.GNLVIKK.FVSEA.LD.RRKR.QEEWEK....ED.EEC..E....P..LYERLQEQKDRKQ.E.E
Retrocopy DGGDAGNLVIKKSFVSEAGLD*RRKRTQEEWEKIQRQEDLEECQ>EKLMTP-GLYERLQEQKDRKQPE*E

Parental  EQFKFKNMVRGLDEDETNFLDEVSRQQELLEKQRREEELKELKEYRSNLSKVGISSENKKEVEKKLTVKP
          EQFKFK.MVRGLDEDETNFLD.VSRQQEL.EKQ..EEELKELKEYRSNLSK.G..SENK.EVEKK.TVKP
Retrocopy EQFKFKTMVRGLDEDETNFLDKVSRQQELIEKQ*KEEELKELKEYRSNLSKAGLASENKEEVEKKRTVKP

Parental  IETKNKFSQAKLLAGAVKPKSSESGNSVKRLKPDPD
          I..KN.FSQAKLLAGAVKP...........LKPDPD
Retrocopy IQSKNTFSQAKLLAGAVKPELRQ--RPL*KLKPDPD

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_175 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175 , retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,