RetrogeneDB ID: retro_ptro_989

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:91138127..91138575(-)
• Located in intron of: ENSPTRG00000006640

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3G
• Ensembl ID: ENSPTRG00000017068
• Aliases: None
• Description: None

Sequence

>retro_ptro_989
ATGGCTGGGAATAAAGGATGAGGATGTGCTGCTTATACCTTTAATATTGAGGCTGTTGGATTTAGCAAAGGTAAAAAGTT
ACCTGATGTAGTGTTGAAACCACCCCCACTATTTCCTGATACAGATTATAAACCAGTGCCACTGAAGACAGGAGAAGGTG
AATAATATATGCTGGCTTTGAAACAGGAGTTGAGAGAAACAATGAAAAGAATGCCCTATTTTATTGAAACACCCTCATGA
AGAAAGACAAGATATCAAAAGGTATAGTAAAAGATACGTGAAGGTATACAAGGAAGAGTGGATACCAGATTGGAGAAGAC
TTCCAAGAGAGATGATGCCAAGAAATAAATGTAAAAAAGCAGGCCCAAAACCCAAAAAGGCAAAAGACACAGGCAAAGGC
ACATCACTCACTAATACTGCAGATGTGTTTAAAAAAATTGAGGAATTG

Alignment

ORF - retro_ptro_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 66.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRGRAAYTFNIEAVGFSKGEKLPDVVLKPPPLFPDTDYKPVPLKTGEGEEYMLALKQELRETMKR
          MAGNKG.G.AAYTFNIEAVGFSKG.KLPDVVLKPPPLFPDTDYKPVPLKTGEGE.YMLALKQELRETMKR
Retrocopy MAGNKG*GCAAYTFNIEAVGFSKGKKLPDVVLKPPPLFPDTDYKPVPLKTGEGE*YMLALKQELRETMKR

Parental  MPYF-IETP-EERQDIERYSKRYMKVYKEEWIPDWRRLPREMMPRNKCKKAGPKPKKAKDAGKGTSLTNT
          MPYF....P.EERQDI.RYSKRY.KVYKEEWIPDWRRLPREMMP...............D.GKGTSLTNT
Retrocopy MPYF>LKHPHEERQDIKRYSKRYVKVYKEEWIPDWRRLPREMMPXXXXXXXXXXXXXXXDTGKGTSLTNT

Parental  EDVLKKMEEL
          .DV.KK.EEL
Retrocopy ADVFKKIEEL

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	0.00 RPM	2.40 RPM
SRP007412_cerebellum	0.00 RPM	5.38 RPM
SRP007412_heart	0.00 RPM	1.40 RPM
SRP007412_kidney	0.00 RPM	2.30 RPM
SRP007412_liver	0.00 RPM	2.98 RPM
SRP007412_testis	0.00 RPM	6.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_989 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_989 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1454
Gorilla gorilla	retro_ggor_1119

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006306	1 retrocopy	retro_chof_125,
Callithrix jacchus	ENSCJAG00000010747	1 retrocopy	retro_cjac_2691,
Echinops telfairi	ENSETEG00000008379	1 retrocopy	retro_etel_1040,
Homo sapiens	ENSG00000113356	2 retrocopies	retro_hsap_1454, retro_hsap_1885,
Gorilla gorilla	ENSGGOG00000000266	2 retrocopies	retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus	ENSMLUG00000014954	1 retrocopy	retro_mluc_2233,
Macaca mulatta	ENSMMUG00000018972	1 retrocopy	retro_mmul_1332,
Nomascus leucogenys	ENSNLEG00000013749	1 retrocopy	retro_nleu_1807,
Otolemur garnettii	ENSOGAG00000005560	1 retrocopy	retro_ogar_3512,
Pongo abelii	ENSPPYG00000015624	1 retrocopy	retro_pabe_1564,
Pan troglodytes	ENSPTRG00000017068	2 retrocopies	retro_ptro_1266, retro_ptro_989 ,
Rattus norvegicus	ENSRNOG00000016260	2 retrocopies	retro_rnor_458, retro_rnor_503,
Ictidomys tridecemlineatus	ENSSTOG00000008664	1 retrocopy	retro_itri_18,
Tupaia belangeri	ENSTBEG00000002278	2 retrocopies	retro_tbel_2495, retro_tbel_3069,