RetrogeneDB ID: retro_mmul_544

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:160104164..160104999(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSMMUG00000014475
• Aliases: None
• Description: ribonuclease H1 precursor [Source:RefSeq peptide;Acc:NP_001244787]

Sequence

>retro_mmul_544
GTGAGCCATGTGCCAGCCTTGATAGCTGTGCGCTGCCGCAGAGACCGTTGCAGCCTCAGGATGGCCTATGCTGTGGGGAG
GGCCTGCAGGACCGGGGTCTTTCTGACCTGGAGTGAATGTAGAGCATAGGTGGACCTATTTCCTGCTGCCAGATTTAAGA
AGTTTGCCACAGAAAATGAGGCCTGGGCCTTTGTCAGGAAATCTGCAAGCCCAGAAGGTTCAGAAGGGCAGAAAAATAAA
CATGTACAAGAATCACAAACGAAAGCCATCAAGGGACTCCATGAGCCATTGAATGGCGATGGAGATGAAAGCGCAGAGTC
GTGTGCAAAGCCTGTGAAGCAAATCACAGAGCCGGCACCTCGAATGAGCAGGGACATTTTCTTACATCGAAGGCTTTCTC
GTCGAGTACACTGATGGCTGCTGCTCCAGTAACGGGTGGAGGAGAGCACTTGTGGGAACTGATGTTTACTGGGGGCCAGG
CCATCCTTTAAATGTAGGCATTAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAAAATCATGCAGCCTGCAACACCA
TTGAACAAGGAGAGGCTGAAAACATCAAAAAATTGGTTCCGTACACAGATAGTATGTTTACTGTAAATAGTATAACTAAC
TGGGTTCAAGGTAGGAAGAAGAACAGGTGGAAGACAAGTACAGGGAAAGAGGTGATGAACAAAGAGGACTTTGTGGCACT
GGAGAAGCTCACTCAAAGCATGGGCATTCAGTGGATACTTGTTCCTGGTCATCCAGGGTTTATCGGGAATGAAAAAGCTG
ATAGATTAGCAAGAGGAGCTAAACATTCTGAAGAC

Alignment

ORF - retro_mmul_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.62 %
• Parental protein coverage: 97.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAHRVALAAVSCRCGSRGFGMFYAVRRGRKTGVFLTWNECKAQVDRFPAARFKKFATEDEAWTFVRKSAS
          ..H..AL.AV.CR.......M.YAV.R...TGVFLTW.EC.A.VD.FPAARFKKFATE.EAW.FVRKSAS
Retrocopy VSHVPALIAVRCRRDRCSLRMAYAVGRACRTGVFLTWSECRA*VDLFPAARFKKFATENEAWAFVRKSAS

Parental  PEVSEGQENQHGQELQMKASKRLREPLDGDGDESAEPYAKHMKPSMEPAPPVSRDTFSYM-GDFVVVYTD
          PE.SEGQ.N.H.QE.Q.KA.K.L.EPL.GDGDESAE..AK..K...EPAP..SRD.F....G..V.....
Retrocopy PEGSEGQKNKHVQESQTKAIKGLHEPLNGDGDESAESCAKPVKQITEPAPRMSRDIFLHR>GFLVEYTDG

Parental  GCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKAQNISKLVLYTDSMFTI
          .C.S.NG.RR...G..VYWGPGHPLNVGIRLPG.QTNQRAE.HAAC..IEQ..A.NI.KLV.YTDSMFT.
Retrocopy CCSS-NGWRRALVGTDVYWGPGHPLNVGIRLPG*QTNQRAENHAACNTIEQGEAENIKKLVPYTDSMFTV

Parental  NGITNWVQSWKENGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARKGAKQLE
          N.ITNWVQ..K.N.WKTS.GKEV.NKEDFVALE.LTQ.M.IQW..VPGH.GFIGNE.ADRLAR.GAK..E
Retrocopy NSITNWVQGRKKNRWKTSTGKEVMNKEDFVALEKLTQSMGIQWILVPGHPGFIGNEKADRLAR-GAKHSE

Parental  D
          D
Retrocopy D

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	12.89 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.76 RPM
SRP007412_cerebellum	0.00 RPM	13.95 RPM
SRP007412_heart	0.00 RPM	18.37 RPM
SRP007412_kidney	0.00 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	8.27 RPM
SRP007412_testis	0.00 RPM	26.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_544 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_544 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_300
Pan troglodytes	retro_ptro_244
Gorilla gorilla	retro_ggor_336

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544 , retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,