RetrogeneDB ID: retro_mmul_567

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:186106972..186107757(-)
• Located in intron of: ENSMMUG00000005409

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT2B
• Ensembl ID: ENSMMUG00000010394
• Aliases: None
• Description: None

Sequence

>retro_mmul_567
GCTCAAGGTGAAAATTTACAAAGACTAGAGTCTCACATTCAAATGCTTGATGGAGTCAATGTGACAACAGCTGCACCCAA
ATCTGAGGGGCTGCTTGTCTTCTCTATCCTACTATACCATCTCCTGTCATCAGTGGCTACAGAAATAAGTCTACCTTCTC
TGTGAATCAAGGTCCAGATGGCAATCCAAAGACTGTGGGATATGACCTGGGAACCTGAAAAGATGGGAACATCGTCTGTG
TACAGTCTACCCATCTGAAAAACATCCCTTAGAAACACAATCAGGTGGCACAGTACGATGAAGTATTCCTTCCACAGTCT
CCAACAGAGCCCCGCCTTCTGCTTCATGAAGGTTGATACTGGTGTGAGCTCACAGTCCGCACCAATAGCCTAAGGCACAC
AATGGCTGTCATCACATTCCATCCCCAGGAATTAAGTCCAGGGGAGCTCGGTGTTCAGAAGGAGACTGTAAAGGAATTTT
TCATTAAAAGTCCTGGAGCCGTCCATGACTTGACCTCAACTGACTTCCAGGAAAGCACCATGACCCGTTTCAGCCATCAT
CAGTCCGCCTACTAGCTCTTGTTTGGGGAACCTCATATCTTTAAAGATCTCCTGGGCTTGAAAGTCTGCATTTCTCCAGA
TGCCTTTTTCCAGATTAACACTGCTGGTGCAGAGATGCTGTACTGGATTGTAGGGAAGCTGAGTGGAGTGAACTCTAACA
CCATCCTCCTTGCCATCTGCTGTGGAACTGGTGTGATCAGCCTCCCTCTGGCTCAGCACGTCGCA

Alignment

ORF - retro_mmul_567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.47 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQKKILQRLESYIQMLNGVNVTTAVPKSESL-PCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGYY
          AQ...LQRLES.IQML.GVNVTTA.PKSE.L..CLL.P.IPSPVI.GYRNKSTFSVN.GPDGNPKTVGY.
Retrocopy AQGENLQRLESHIQMLDGVNVTTAAPKSEGL<ACLLYPTIPSPVISGYRNKSTFSVNQGPDGNPKTVGYD

Parental  LGTWRDGNIVCVRSNNLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELIVRTNSQGHTMAIIT
          LGT..DGNIVCV.S..LKNIP.KH.QVAQY.EVFL.QSP.EP.L..HEG.YW.EL.VRTNS..HTMA.IT
Retrocopy LGT*KDGNIVCVQSTHLKNIP*KHNQVAQYDEVFLPQSPTEPRLLLHEG*YWCELTVRTNSLRHTMAVIT

Parental  FHPQKLSQEELHVQKETVKEFFIRGPGAACDLTSLYFQESTMTRCSHQQSPYQLLFGEPYIFEELLSLKI
          FHPQ.LS..EL.VQKETVKEFFI..PGA..DLTS..FQESTMTR.SH.QS.Y.LLFGEP.IF..LL.LK.
Retrocopy FHPQELSPGELGVQKETVKEFFIKSPGAVHDLTSTDFQESTMTRFSHHQSAY*LLFGEPHIFKDLLGLKV

Parental  RISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGKSVIGLSLAQHTS
          .ISPDAFFQINTAGAEMLY..VG.L.GVNS.TILL.ICCGTG..VI.L.LAQH..
Retrocopy CISPDAFFQINTAGAEMLYWIVGKLSGVNSNTILLAICCGTG--VISLPLAQHVA

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	5.83 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	6.11 RPM
SRP007412_cerebellum	0.26 RPM	2.78 RPM
SRP007412_heart	0.00 RPM	7.24 RPM
SRP007412_kidney	0.00 RPM	11.97 RPM
SRP007412_liver	0.04 RPM	6.65 RPM
SRP007412_testis	0.00 RPM	1.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_567 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_567 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_567 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_272
Pan troglodytes	retro_ptro_228
Gorilla gorilla	retro_ggor_319
Pongo abelii	retro_pabe_397

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004570	1 retrocopy	retro_cjac_1676,
Homo sapiens	ENSG00000188917	1 retrocopy	retro_hsap_272,
Gorilla gorilla	ENSGGOG00000023759	1 retrocopy	retro_ggor_319,
Macropus eugenii	ENSMEUG00000006532	2 retrocopies	retro_meug_1325, retro_meug_74,
Macaca mulatta	ENSMMUG00000010394	1 retrocopy	retro_mmul_567 ,
Monodelphis domestica	ENSMODG00000025630	1 retrocopy	retro_mdom_77,
Nomascus leucogenys	ENSNLEG00000007522	1 retrocopy	retro_nleu_1485,
Pongo abelii	ENSPPYG00000020545	1 retrocopy	retro_pabe_397,
Pan troglodytes	ENSPTRG00000023413	1 retrocopy	retro_ptro_228,