RetrogeneDB ID: retro_mmul_1674

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:32133138..32133620(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1643
• Ensembl ID: ENSMMUG00000020474
• Aliases: None
• Description: DNA-directed RNA polymerase II subunit RPB3 [Source:RefSeq peptide;Acc:NP_001245048]

Sequence

>retro_mmul_1674
AATGTCAAGTTCATCATCCAGAACACCAACCCGGCAGTGGCTATTTCGATTCGGAGTGTCTTCTCGCTGAGGTGCCCATA
ATAGTCATTGACTGGGTTCAAATTGATGCCAATTCCTCAGTTATTCATGATGAGTTCATGGCTCGCAAACTTAGATTAGT
TCTCCTCATTAGTGATGACATTGTAGACAAGCTGCTATCCTCCTGGGACTTCCCATGTGAAGAGTTCTGCTAGTGCTTGG
TGGAGTTCACCCTCGATGTGCAGTGCAATGAAAAGCAGACTTGACATGTCGTGTCTTGAGACCTCATCTCCAACAGCCCC
CAGGTCATTCCAGTGAACCAAGATGATGACCCTAATGACTACGTGGAGCAGGATGACATTCTCATCATCAAGTTGAGAAA
GGGCCAGGAGCTGAGACTTTGAGCCTATACGAAAAAATGCTTTAGCAAGGAGTATGTTAAGTTGAACCCTACTGCAGGGG
TG

Alignment

ORF - retro_mmul_1674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.7 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVKFIIENTDLAVANSIRRVF-IAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLISDDIVDKLQYSR
          NVKFII.NT..AVA.SIR.VF..AEVPII.IDWVQIDANSSV.HDEF.A..L.L..LISDDIVDKL..S.
Retrocopy NVKFIIQNTNPAVAISIRSVF<LAEVPIIVIDWVQIDANSSVIHDEFMARKLRLVLLISDDIVDKLLSSW

Parental  DCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKG
          D..CEEFC..C.VEFTLDV.CNE.QT.HV.S.DLISNSP.VIPV...N.D.DPNDYVEQDDILI.KLRKG
Retrocopy DFPCEEFC-*CLVEFTLDVQCNEKQT*HVVS*DLISNSPQVIPV---NQDDDPNDYVEQDDILIIKLRKG

Parental  QELRLRAYAKKGFGKEHAKWNPTAGV
          QELRL.AY.KK.F.KE..K.NPTAGV
Retrocopy QELRL*AYTKKCFSKEYVKLNPTAGV

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	44.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	52.91 RPM
SRP007412_cerebellum	0.13 RPM	41.91 RPM
SRP007412_heart	0.06 RPM	29.44 RPM
SRP007412_kidney	0.00 RPM	50.59 RPM
SRP007412_liver	0.04 RPM	35.19 RPM
SRP007412_testis	0.00 RPM	30.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1674 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1674 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1674 has 0 orthologous retrocopies within eutheria group .

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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,