RetrogeneDB ID: retro_mmul_1332

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:41523148..41523592(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3G
• Ensembl ID: ENSMMUG00000018972
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide G (32kD) [Source:HGNC Symbol;Acc:30075]

Sequence

>retro_mmul_1332
ATGGCTGGGAATAAAGGAAGAGGAGGATGTGCTGCTTATACCTTTAATATTGAGGCTGTTGGATTTAGCAAAGGTGAAAA
GTTACCTTATGTAGTGTTGAAACCACCCCCACTATTTCCTGATGCAGATTATAAATCGGTGGCACTGAAAACAGAAAATG
AAGAGTATATACTGGCTTTGAAACAGGAGTTGAGAGAAACAATGAAAAGAATGCCTTATTTTATTGAAACACCTGAAGAA
TGACAAGATATTGAAAGGTATAGTAAAAGATACATGAAGGTATATAAGGAAGAATAGATACCAGATTGGAGAAGACTTCC
AAGAGAGATGATGTCAAGAAATAAATGTAAAAACACAGGCCCAAAACCCAAAAAGGCAAAAGACGCAGGCAAAGGCACTT
CACTCACTAATACTTCAGATGTGTTGAAAAAAATTGAGGAATTG

Alignment

ORF - retro_mmul_1332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRGR-AAYTFNIEAVGFSKGEKLPDVVLKPPPLFPDTDYKPVPLKTGEGEEYMLALKQELRETMK
          MAGNKGRG..AAYTFNIEAVGFSKGEKLP.VVLKPPPLFPD.DYK.V.LKT.E.EEY.LALKQELRETMK
Retrocopy MAGNKGRGGCAAYTFNIEAVGFSKGEKLPYVVLKPPPLFPDADYKSVALKT-ENEEYILALKQELRETMK

Parental  RMPYFIETPEERQDIERYSKRYMKVYKEEWIPDWRRLPREMMPRNKCEKAGPKPKKAKDAGKGTSLTNTA
          RMPYFIETPEE.QDIERYSKRYMKVYKEE.IPDWRRLPREMM.RNKC...GPKPKKAKDAGKGTSLTNT.
Retrocopy RMPYFIETPEE*QDIERYSKRYMKVYKEE*IPDWRRLPREMMSRNKCKNTGPKPKKAKDAGKGTSLTNTS

Parental  DVLKKIEEL
          DVLKKIEEL
Retrocopy DVLKKIEEL

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	0.00 RPM	7.40 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.41 RPM
SRP007412_cerebellum	0.00 RPM	9.23 RPM
SRP007412_heart	0.00 RPM	3.18 RPM
SRP007412_kidney	0.00 RPM	3.64 RPM
SRP007412_liver	0.00 RPM	1.50 RPM
SRP007412_testis	0.00 RPM	2.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1332 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1332 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,