RetrogeneDB ID: retro_mmul_799

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:34072855..34073712(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019280
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_799
ATGAGCTGGTTTGTGTTCCTGCCCCACAGAGTCGCCTTGGTTGCCGTGTCCTGCCCTCGCAGTTCTCCCGGGTTCGGGAT
GTTCTATGCCGTGAGGAGGGGCTGTAAGACCGGGGTCTTTCTGACCTGGAATGAGTGCAAAGCACAGGTGGACCAGTTTC
CTGCTGCCAGATTTAAGAAGTTTGCCACAGAGGATGAGGCCTGGACCTTTGTCAGGAAATCTGCAAGTCTGGAAGTTTCA
GAAGGGCAGGAAAATCAACATGGACAAGAATCGCAGATGAAAGCCAGCAAGCCACTCTGTGAGTCACTGGATGGAGATGG
AGATGAAAGCACAGAGCCTATGCAAAGTACATGAAGCAGAGCATGGAGCTGGCGCCTCCAGTTAGCAGAGACAAGGTTTC
CTACATGGGAGACTTTGTTGTCATCTACACTGATGGCTGCTGCTACAGTAATGGGCATAAAAGGCAAGGAGCAGGAATCT
GTGTTTACTGGGGGCCAGGCCATCCTTTAAATGTAGGCATTAGACTTCCTGGGCGACAGACAAACCAAAGAGCAGAAATC
CATGCAGCCTGCAAAACCATTGAACAAGCAAAGGCTCAAAACATCAGTAAACTGGTTCTGTATACAGACAGTATGTTTAC
TATAAATGGTATAACTAACTGTGTTCAAAGTTGGAAGGAAAATGGGTGGAAGACAAGTGCAGGGAAAGAGGTGATCAACA
AAGAGGACTTCGTGGCACTGGAGAGGCTCAGTCAGGGGATGGACATTCAGTGGATGCACGTTCCTGGTCATTCGGGATTT
ATAGGCAATGAAGAAGCTGGTAGATTAGCCAGAGAAGGAGCTAAACAATCGGAAGAC

Alignment

ORF - retro_mmul_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSWLVFLAHRVALAAVSCRCGSRGFGMFYAVRRGRKTGVFLTWNECKAQVDRFPAARFKKFATEDEAWTF
          MSW.VFL.HRVAL.AVSC...S.GFGMFYAVRRG.KTGVFLTWNECKAQVD.FPAARFKKFATEDEAWTF
Retrocopy MSWFVFLPHRVALVAVSCPRSSPGFGMFYAVRRGCKTGVFLTWNECKAQVDQFPAARFKKFATEDEAWTF

Parental  VRKSASPEVSEGQENQHGQELQMKASKRLREPLDGDGDESAEP-YAKHMKPSMEPAPPVSRDTFSYMGDF
          VRKSAS.EVSEGQENQHGQE.QMKASK.L.E.LDGDGDES.EP.YAK.MK.SME.APPVSRD..SYMGDF
Retrocopy VRKSASLEVSEGQENQHGQESQMKASKPLCESLDGDGDESTEP<YAKYMKQSMELAPPVSRDKVSYMGDF

Parental  VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKAQNISKLVLYT
          VV.YTDGCC.SNG..R..AGI.VYWGPGHPLNVGIRLPGRQTNQRAEIHAACK.IEQAKAQNISKLVLYT
Retrocopy VVIYTDGCCYSNGHKRQGAGICVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKTIEQAKAQNISKLVLYT

Parental  DSMFTINGITNWVQSWKENGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARK
          DSMFTINGITN.VQSWKENGWKTSAGKEVINKEDFVALERL.QGMDIQWMHVPGHSGFIGNEEA.RLAR.
Retrocopy DSMFTINGITNCVQSWKENGWKTSAGKEVINKEDFVALERLSQGMDIQWMHVPGHSGFIGNEEAGRLARE

Parental  GAKQLED
          GAKQ.ED
Retrocopy GAKQSED

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	0.24 RPM	18.37 RPM
SRP007412_kidney	0.00 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	8.27 RPM
SRP007412_testis	0.11 RPM	26.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_799 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_799 has 0 orthologous retrocopies within eutheria group .

---

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,