RetrogeneDB ID: retro_mmul_1769

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:67035892..67036642(+)
• Located in intron of: ENSMMUG00000029592

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM192
• Ensembl ID: ENSMMUG00000021912
• Aliases: None
• Description: transmembrane protein 192 [Source:HGNC Symbol;Acc:26775]

Sequence

>retro_mmul_1769
GGTTTCTTGGATATCACTCAAAGTATTGAAGATGACCCAGCTCTGGATACCCAGCTTCTCTTAACATTACTCACTAGAAG
CTCATTTTAGACCCTGATTCTTTTTCCTACAGTCGTCATAGAAAGTCTTCTCTTGTTTATTCATGTTGTGTTACTTTTAG
CGTTTTTAACAGATGTGGTTTGTTCTTACCCTAATCTAAATGAAGACAGGTGCCCAGGATACTACACCAACCCTCTTAAA
GTTCAAATGGTCGTAATCCTTGGGAAAGTTATTTTGTGGTGGATATTCCATTTACATCTTGAATGGTACATCCAGTATCA
CCACAGCAAAGTCAGAAATCGAGGCTATAACTTGATCTACTGATGTATAAGGCATCTCAAGAAATTTGCATTAATGATAC
ACTCCACTGGTAACAATAATTATCTTCATACTGTGTTGCAGCAATTCCTTCCTGGAACCCAGCAGATCAGATTATATCTT
GATCTCCTTCTGGACATCCTGGCTCTGGAGCTGATCTGTTTTCTGATGTGTCTGCTCATTTACACAGTGAAAATCTGGAA
ATTTAATAAAGCTAAATCATATCCTGATGTACTTGAAGAGGGAAAAATCTATACATAACCCAGCAGTATTACCTTGGAAA
CTGGATTCAGAACTATTTGAAACCTAGAAGAAATTGTTGAAAAGCAAGGAGACATAGTAGTATATATGAAGTGACACAAT
GAAGTGTTGAGTGACTGTTGACTCTCACTT

Alignment

ORF - retro_mmul_1769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.37 %
• Parental protein coverage: 92.25 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSLDITQSIEDDPLLDAQLLP-HHSLQAHFRPRFHPLPT-VIIVNLLWFIHLVFVILAFLTGVLCSYPNP
          G.LDITQSIEDDP.LD.QLL..H.SL.AHFRP.F..L...VI...LL..IH.V...LAFLT.V.CSYPN.
Retrocopy GFLDITQSIEDDPALDTQLLL>HYSLEAHFRP*FFFLQS<VIESLLLF-IHVV-LLLAFLTDVVCSYPNL

Parental  NEDKCPGNYTNPLKVQTVIILGKVIL-WILHLLLECYIQYHHSKIRNRGYNLIYRSTRHLKRLALMIHSS
          NED.CPG.YTNPLKVQ.V.ILGKVIL.WI.HL.LE.YIQYHHSK.RNRGYNLIY...RHLK..ALMIHS.
Retrocopy NEDRCPGYYTNPLKVQMVVILGKVILWWIFHLHLEWYIQYHHSKVRNRGYNLIY*CIRHLKKFALMIHST

Parental  GNT-VLLLILCMQHSFPEPGR-LYLDLILALLALEL--ICSLICLLIYTVKIQRFNKAKPEPDILEEEKI
          GN........C...SF.EP.R...L.L.L.L..L.L..IC.L.CLLIYTVKI..FNKAK..PD.LEE.KI
Retrocopy GNN>IIFIL-CCSNSFLEPSR<IRLYLDLLLDILALELICFLMCLLIYTVKIWKFNKAKSYPDVLEEGKI

Parental  YAYPSNITSETGFRTISGLEEIVEKQGDTIEYLKRHNALLSKRLLAL
          Y..PS.IT.ETGFRTI..LEEIVEKQGD...Y.K.HN..LS...L.L
Retrocopy YT*PSSITLETGFRTI*NLEEIVEKQGDIVVYMK*HNEVLSDC*LSL

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	9.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.77 RPM
SRP007412_cerebellum	0.13 RPM	7.04 RPM
SRP007412_heart	0.00 RPM	6.18 RPM
SRP007412_kidney	0.00 RPM	17.49 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.04 RPM	2.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1769 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1769 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3483
Pan troglodytes	retro_ptro_2357
Pongo abelii	retro_pabe_2878

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009198	1 retrocopy	retro_cjac_2346,
Homo sapiens	ENSG00000170088	1 retrocopy	retro_hsap_3483,
Macaca mulatta	ENSMMUG00000021912	1 retrocopy	retro_mmul_1769 ,
Nomascus leucogenys	ENSNLEG00000006475	1 retrocopy	retro_nleu_2203,
Pongo abelii	ENSPPYG00000015175	1 retrocopy	retro_pabe_2878,
Pan troglodytes	ENSPTRG00000016571	1 retrocopy	retro_ptro_2357,
Ictidomys tridecemlineatus	ENSSTOG00000000402	1 retrocopy	retro_itri_1414,