RetrogeneDB ID: retro_pabe_1564

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:60878471..60879126(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3G
• Ensembl ID: ENSPPYG00000015624
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075]

Sequence

>retro_pabe_1564
ATGGCTGGGAATAAAGGAAGAGGATAATGTGCTGCTTATACCTTTAATATTGAGGCTGTTGGATTTAGCAAAGGTGAAAA
GTTACCTTATGTAGTGTTGAAACCACCCCCACTATTTCCTGATGCAGATTATAAATCAGTGTCACTGAAAACAGAAGATG
AAGGATATATGCTGGCTTTGAAACCGGAGTTGAGAGAAACAATGAAAAGAATGCCTTATTTTATTGAAACACCTGAAGAA
AGACAAGATATTGAAAGGTATAGTAAAAGATACATGAAGGTATATAAAGAAGAATGGATACCAGATTGGAGAAGACTTCC
AAGAGAGAGAATGCCAAGAAATAAATGTAAAAACACAGGCCCAAAACCCAAAAAGGCAAAAGACACAGGCAAAGGCACTT
CACTAATACTTCAGAGGTGTTGAAAAAATTGAGGAATTGGGAAAGAAAGGTGATGGTGAAAATTCAGATGAGGAAAATGA
AAAGGAAGAAGGAAGCAAAGAGGAAAGTAAAGAAGGTGATGATGACGATGACAATGATGCTGCAGAACAGGAAGGATATG
ATGAAGAAGAGGAAAATGACTACATTAATTCATACTTTGAAGATGGAAATGATTTTGGCCCAGACAGTGATGACAACGTG
TATGAAGCAACCTAT

Alignment

ORF - retro_pabe_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRG-RAAYTFNIEAVGFSKGEKLPDVVLKPPPLFPDTDYKPVPLKTGEGEEYMLALKQELRETMR
          MAGNKGRG..AAYTFNIEAVGFSKGEKLP.VVLKPPPLFPD.DYK.V.LKT.E.E.YMLALK.ELRETM.
Retrocopy MAGNKGRG*CAAYTFNIEAVGFSKGEKLPYVVLKPPPLFPDADYKSVSLKT-EDEGYMLALKPELRETMK

Parental  RMPYFIETPEERQDVERYSKRYMKVYKEEWIPDWRRLPREMMPRNKCKKAGP-KPKKAKDAGKGTSLTNT
          RMPYFIETPEERQD.ERYSKRYMKVYKEEWIPDWRRLPRE.MPRNKCK..GP.K..K.K........TNT
Retrocopy RMPYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPRERMPRNKCKNTGP<KTQKGK-RHRQRHFTNT

Parental  ADVLKK-IEELEKRGDGEKSDEENEEKEGSKEKSKEGDDDDDDDAAEQEEYDEEEQEEENDYINSYFEDG
          ..VLKK.IEEL.K.GDGE.SDEENE..EGSKE.SKEGDDDDD.DAAEQE.YDEEE...ENDYINSYFEDG
Retrocopy SEVLKK<IEELGKKGDGENSDEENEKEEGSKEESKEGDDDDDNDAAEQEGYDEEE---ENDYINSYFEDG

Parental  DDFGADSDDNMDEATY
          .DFG.DSDDN..EATY
Retrocopy NDFGPDSDDNVYEATY

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	1.44 RPM
SRP007412_cerebellum	0.00 RPM	4.01 RPM
SRP007412_heart	0.00 RPM	1.17 RPM
SRP007412_kidney	0.00 RPM	1.66 RPM
SRP007412_liver	0.00 RPM	1.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1564 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1564 has 0 orthologous retrocopies within eutheria group .

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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,