RetrogeneDB ID: retro_ptro_1448

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:1215088..1215618(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2C
• Ensembl ID: ENSPTRG00000008157
• Aliases: None
• Description: None

Sequence

>retro_ptro_1448
GAGTGCTTGGTGGAGTTCACCCTCGATGTGCAGTGCAATGACGACCAGATTTGACATGTCACATCTTGAGACCTCATCTC
CAACAGCCCCCAGGTCATTCCAGTGAAACAAGATGATGACCCTAATGACTACGTGGAGCAGGATGACATTCTCATAATCA
AGTTGAGAAAGGGCCAGGAGCTGAGACTTTGAGCCTATACGAAAAAGTGTTTTAGCAAGGAACATGCCAAGTTGAACCTT
ACTGCAGGGGTGGCTTTTGAATACAATCCAGACAATGCCATGAGGCATGCAGTGTACCCCAAACCCAAGGAGTGGCCAAA
GAGTGAGCACTTGGAGCTGGATGAGGATGAGTCACAGGTGCCCTGTGACCCCATGGGCAAGCCAGAAAGGTTTTACTACA
ACATGAATTCCTATGGCTCTCTGTGTCCTTAAACCATGTGCTCTTAGCCCTCACTGGATTGAAGAAGAAGCTGAGTGATT
TACAAACTCAATTAAGCCACGAGATCCAGAGTGACATGCTAACTATAAAC

Alignment

ORF - retro_ptro_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.45 %
• 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.DQ..HVTS.DLISNSP.VIPV.....D.DPNDYVEQDDILI.KLRKGQELRL.AY.
Retrocopy ECLVEFTLDVQCNDDQI*HVTS*DLISNSPQVIPV---KQDDDPNDYVEQDDILIIKLRKGQELRL*AYT

Parental  KKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVES
          KK.F.KEHAK.N.TAGVAFEY.PDNA.RH.VYPKP.EWPKSE..ELDEDESQ.P.DP.GKPERFYYN..S
Retrocopy KKCFSKEHAKLNLTAGVAFEYNPDNAMRHAVYPKPKEWPKSEHLELDEDESQVPCDPMGKPERFYYNMNS

Parental  CGSLRPETI-VLSALSGLKKKLSDLQTQLSHEIQSDVLTIN
          .GSL.P.T..VL.AL.GLKKKLSDLQTQLSHEIQSD.LTIN
Retrocopy YGSLCP*TM<VLLALTGLKKKLSDLQTQLSHEIQSDMLTIN

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	0.05 RPM	48.96 RPM
SRP007412_cerebellum	0.00 RPM	59.65 RPM
SRP007412_heart	0.00 RPM	34.45 RPM
SRP007412_kidney	0.00 RPM	71.47 RPM
SRP007412_liver	0.00 RPM	52.05 RPM
SRP007412_testis	0.00 RPM	35.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1448 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1448 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2496
Gorilla gorilla	retro_ggor_1557
Pongo abelii	retro_pabe_1839
Callithrix jacchus	retro_cjac_2026

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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 ,