RetrogeneDB ID: retro_mmul_2449

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:62350589..62351256(-)
• Located in intron of: ENSMMUG00000022237

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSMMUG00000023226
• Aliases: None
• Description: None

Sequence

>retro_mmul_2449
ATCATCAACATCAAAAAAGAGAAGAAAGAGATGGATGAAGACACGAAACATCTCACCATGCTGGAAAAGGACGATTTCAT
CGATGACCCCAGGCTGAGGAATGACACTCGAAACATGCCTGTGCAGCTGTCATTGGCTCACTCAGGGTGGCTTTTTAAGG
AAGAAAATGATGAACCAGTTGTTAAACCTTGGCTGGCTGGCCCCAAGGAAGAGGTAGGTGTACCTACTGTGAAATTGAAA
GAGGAGCCACAAGATGAGGAGGAGGAGGCCAAGATGAAGGCTCCTCCCAGAGCAGCCAGGAAGGCTCCCTGGCCTCCCGA
AGGACATACCTGTGGCAGAGCTGCTCAGGGAGCTGAGCCTCACCAAGGAGGAACTGCTGTTCCTCCAGCTGCCAGACAAC
TCTCCCTGGCCACCCACCACCCAGCTCATCAAGGCAGAGGTGCAGGGCGAGGATAGACAGGTGGTACTCATCAAGCAGGA
GAAAGACCAGGAAGCCAGGCTGGCAGAGAATGCTTCTATCCTAGCTGACCTGACAGAGGGTCAGGTTGGCAAGCTGCCCA
TCCACAAATCCAAAAGGGTGCAACCCCTCCTGGGCAAGGTTACTCTGGATGTGACCATGGGAACCGCCTGCTCTTTCCTG
CAGGAGAGGGTGTCTGTGGGCCTTGGA

Alignment

ORF - retro_mmul_2449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.22 %
• Parental protein coverage: 57.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IINIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKPWLTGPK
          IINIKKEK.E.DE.TK..L.MLEKDDF.DDP.LRNDTRNMPVQL.LAHSGWLFKEENDEP.VKPWL.GPK
Retrocopy IINIKKEKKEMDEDTKH-LTMLEKDDFIDDPRLRNDTRNMPVQLSLAHSGWLFKEENDEPVVKPWLAGPK

Parental  EEDMEVDVPAVKVKEEPRDEEE-ANMKAPPKAARKTP-GLPKDVSVAELLRELSLTKEEELLFLQLPDTL
          E...EV.VP.VK.KEEP.DEEE.A.MKAPP.AARK.P.GLPKD..VAELLRELSLTKEE.LLFLQLPD..
Retrocopy E---EVGVPTVKLKEEPQDEEEEAKMKAPPRAARKAP>GLPKDIPVAELLRELSLTKEE-LLFLQLPDNS

Parental  PGQPPTQDIKPIKTEVQGEDGQMMLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVT
          P..P.TQ....IK.EVQGED.Q..LIKQEKD.EA.LAENA..LADLTEGQVGKL.I.KS.RVQ.LLGKVT
Retrocopy PWPPTTQ---LIKAEVQGEDRQVVLIKQEKDQEARLAENASILADLTEGQVGKLPIHKSKRVQPLLGKVT

Parental  LDVTMGTACSFLQELVSVGLG
          LDVTMGTACSFLQE.VSVGLG
Retrocopy LDVTMGTACSFLQERVSVGLG

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	0.11 RPM	12.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.06 RPM
SRP007412_cerebellum	0.00 RPM	10.46 RPM
SRP007412_heart	0.00 RPM	10.83 RPM
SRP007412_kidney	0.00 RPM	10.80 RPM
SRP007412_liver	0.04 RPM	8.23 RPM
SRP007412_testis	0.00 RPM	81.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2449 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2449 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_596
Pan troglodytes	retro_ptro_439
Pongo abelii	retro_pabe_594

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449 ,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,