RetrogeneDB ID: retro_opri_445

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_122818:447..1272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2C
• Ensembl ID: ENSOPRG00000006979
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Source:HGNC Symbol;Acc:9189]

Sequence

>retro_opri_445
ATGCCGTAGGCCAATCAGCCCACCGTGCACGTCACCAAGCTCACAGACGAGAACGTCAAGTTCATCATCGAGAATACTGA
CCTGGCGGTGGCCAATTCCATCCAGAGGGTCTTCATCGCCGAGGTGCCTATAATAGCCATTGACTGGGTTCAGATCGACG
CCAATTCCTCTGTCCTTCATGATGAATGCATTGCTCACAAGCTTGGATTGATCCCTCTTACTAGTGACGACATCGTGGAC
AAGTTGCAGAACTCTCGGGACTGCACCTGCGAGGAGTTCTGCCCTGAGTGCTCAGTGGAGTTCACCCTCGACGTGCGTTG
TAATGAAGATCAGACCCGCCACATCACATACCAGGACCTCATCTCCAACAGCCCTCGGGTCATTCCGGTGACATCCCGGA
ACCGGGACAATGACCCCAACGACTACGCGGAGCAGGATGACATCCTCATCGTCAAGCTGAGAAAGGGCCAGGAGCTGAGG
CTTCGAGCTACGCCAAAAAGGGCTTTCTGCAAGGAACATGCCAAGTGGAACCCCACTGCAGGGGTGGCTTTGAATACTAT
CCCAGATAATGCCCTGAGGCACACCGTGTACCCCAAGCCTGAGGAATGGCCCCAAGAGTGAGTACTCAGAGCTGGACGAG
GACGAGTCCCAGGCTCCTATGACCCCAACGGCAAGCCAGAGAGGTTCTACTACAACGTGGAATCCTGTGGCTCTCTGCGG
CCCGAAACCATCGTGCTGTCAGCGCTCTCCAGGCTGAAGAAGCAGCTAAGTGATCTGCAGACTCAGTTGAGCCACGAGAT
CCAGCGTGACGTGCTAACCATCAAC

Alignment

ORF - retro_opri_445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGL
          MP.ANQPTV..T.LTDENVKFIIENTDLAVANSI.RVFIAEVPIIAIDWVQIDANSSVLHDE.IAH.LGL
Retrocopy MP*ANQPTVHVTKLTDENVKFIIENTDLAVANSIQRVFIAEVPIIAIDWVQIDANSSVLHDECIAHKLGL

Parental  IPLTSDDIVDKLQNSRDCTCEEFCPECSXXXXXXXXXXXXXTRHVTSRDLISNSPRVIPVTSRNRDNDPN
          IPLTSDDIVDKLQNSRDCTCEEFCPECS.............TRH.T..DLISNSPRVIPVTSRNRDNDPN
Retrocopy IPLTSDDIVDKLQNSRDCTCEEFCPECSVEFTLDVRCNEDQTRHITYQDLISNSPRVIPVTSRNRDNDPN

Parental  DYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEW-PKSEYS
          DY.EQDDILIVKLRKGQELRLRA..K..F.KEHAKWNPTAGVA....PDNALRHTVYPKPEEW.PKSEYS
Retrocopy DYAEQDDILIVKLRKGQELRLRATPKRAFCKEHAKWNPTAGVALNTIPDNALRHTVYPKPEEW>PKSEYS

Parental  ELDEDESQAP-YDPNGKPERFYYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHEIQRDVLTIN
          ELDEDESQAP.YDPNGKPERFYYNVESCGSLRPETIVLSALS.LKK.LSDLQTQLSHEIQRDVLTIN
Retrocopy ELDEDESQAP<YDPNGKPERFYYNVESCGSLRPETIVLSALSRLKKQLSDLQTQLSHEIQRDVLTIN

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_445 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
Canis familiaris	ENSCAFG00000008720	1 retrocopy	retro_cfam_688,
Choloepus hoffmanni	ENSCHOG00000002986	1 retrocopy	retro_chof_1988,
Callithrix jacchus	ENSCJAG00000012016	1 retrocopy	retro_cjac_2026,
Dipodomys ordii	ENSDORG00000000081	1 retrocopy	retro_dord_704,
Echinops telfairi	ENSETEG00000004185	1 retrocopy	retro_etel_1953,
Homo sapiens	ENSG00000102978	1 retrocopy	retro_hsap_2496,
Gorilla gorilla	ENSGGOG00000012415	1 retrocopy	retro_ggor_1557,
Myotis lucifugus	ENSMLUG00000015833	2 retrocopies	retro_mluc_129, retro_mluc_236,
Macaca mulatta	ENSMMUG00000020474	1 retrocopy	retro_mmul_1674,
Mus musculus	ENSMUSG00000031783	1 retrocopy	retro_mmus_1723,
Nomascus leucogenys	ENSNLEG00000003034	1 retrocopy	retro_nleu_1431,
Otolemur garnettii	ENSOGAG00000016866	1 retrocopy	retro_ogar_3361,
Ochotona princeps	ENSOPRG00000006979	1 retrocopy	retro_opri_445 ,
Pongo abelii	ENSPPYG00000007390	1 retrocopy	retro_pabe_1839,
Pan troglodytes	ENSPTRG00000008157	1 retrocopy	retro_ptro_1448,