RetrogeneDB ID: retro_pabe_1839

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:14371838..14372368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2C
• Ensembl ID: ENSPPYG00000007390
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Source:HGNC Symbol;Acc:9189]

Sequence

>retro_pabe_1839
GAGTGCTTGGTGGAGTTCACCCTCGATGTGCAGTGCAATGACAACCAGATTTGACATGTCACATCTTGAGACCTCATCTC
CAACAGCCCCCAGGTCATTCCAGTGAACCAAGATGATGACCCTAACGATTACGTGGAGCAGGATGACATTCTCATCATCA
AGTTGAGAAAGGGCCAGGAGCTGAGACTTTGAGTCTATACAAAAAAGTGTTTTAGCAAGGAGCATGCCAAGTTGAACCCT
ACTGCAGGGGTGGCTTTTGAATACAATCCAGACAATGCCATGAGGCATGCAGTGTACCCCAAACCCAAGGAGTGGCCAAA
GAGTGAGCACTTGGAGCGGGATGAGGATGAGTCACAGGTGCCCTGTGACCCCACGGGCAAGCCAGAAAGGTTTTACTACA
ACATGAATTCCTATGGCTCTCTGTGTCCTTAAATGATGTCCTCTTAGCCCTCACTGGATTGAAGAAGAAGCTGAGTGATT
TACAAACTCAATTAAGCCAGGAGATCCAGAGTGACATGCTAACTATAAAC

Alignment

ORF - retro_pabe_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.8 %
• Parental protein coverage: 65.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYA
          EC.VEFTLDV.CN..Q..HVTS.DLISNSP.VIPV...N.D.DPNDYVEQDDILI.KLRKGQELRL..Y.
Retrocopy ECLVEFTLDVQCNDNQI*HVTS*DLISNSPQVIPV---NQDDDPNDYVEQDDILIIKLRKGQELRL*VYT

Parental  KKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVES
          KK.F.KEHAK.NPTAGVAFEY.PDNA.RH.VYPKP.EWPKSE..E.DEDESQ.P.DP.GKPERFYYN..S
Retrocopy KKCFSKEHAKLNPTAGVAFEYNPDNAMRHAVYPKPKEWPKSEHLERDEDESQVPCDPTGKPERFYYNMNS

Parental  CGSLRPETI-VLSALSGLKKKLSDLQTQLSHEIQSDVLTIN
          .GSL.P....VL.AL.GLKKKLSDLQTQLS.EIQSD.LTIN
Retrocopy YGSLCP*MM<VLLALTGLKKKLSDLQTQLSQEIQSDMLTIN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	58.61 RPM
SRP007412_cerebellum	0.00 RPM	61.53 RPM
SRP007412_heart	0.03 RPM	21.40 RPM
SRP007412_kidney	0.00 RPM	78.13 RPM
SRP007412_liver	0.00 RPM	44.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1839 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1839 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2496
Pan troglodytes	retro_ptro_1448
Gorilla gorilla	retro_ggor_1557
Callithrix jacchus	retro_cjac_2026

---

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,