RetrogeneDB ID: retro_mmul_2129

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:14943811..14945154(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000017315
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.313
• Ensembl ID: ENSMMUG00000008172
• Aliases: None
• Description: None

Sequence

>retro_mmul_2129
ACGTTTTTTGCTAAGAATGGTCACTGATGAATGGATTCTAGTATCTATAGCCAGCCCATTCAAACTCAAGCACAGTATGC
CTCCCCAGACTTTAGGCAGCCTGTATATAATCCTCACCAACAGTGCTCGGTCTATAGCATTGTTCCTCAGTTTTGGTCTC
CAAATCCTACACCTTACTTTGAAACACCACTGGCGCCCTTTCCCAATGGTAGTTTTGTGAATGGCTTTAATTCACCAGGA
TCTTATAAAACAAATGCTGCTGCTATGAATATGGGTCGACCATTCCAAAAAATATCTTGCGAAGCCTCATTTTAGGTCAT
CCAGTGGTTCAGAACACTCAACAGAGGACTCTGTGTCATTGGGAGATGGACAATTGAAGATCTAGTTCAAGAAATTTTTC
ACCTGAACAGCATAACCCTACAGTAACTGGGGATTAGGAGCAAACTTAACTTCAAAAGGAGACTTCCACTTTGCAGATGG
AACAGAATGGGGACTATGGTAGAGGCAGAACTCTTTTCAGAGGTCGAAGACGATGACAAGATGACAGGATCTCAAGACCT
CATCCTTCAACAGTTGAATCAAAGGCTCCAACACCAAAGTTTGACTTACTAGCTTCAAATTTTCCACCTTTACCTGGAAG
TTCATCAAGCATCCCAGGTAAACTCATTTCGGAGAATAGGATGTCTGATGTTGTTAAAGGCATCTACAAAGAAAAGGATA
ATGAAGAATTGAGAGTTGGTTGCCCAGTGCCTGCAGATGAGCAGACAGAATGCACTTCTGCCCAGCAACTCAGTATGAGT
ACCAGTTCTTCATGTGCAGCTGAGCTTACTGCATTAAGCACAACTCAGCAAAAAAAGGATCTAATAGAGGATTCCTCTGT
TCAGAAGGATTGTCCCAACCAGACGACTATACCAGTTTCTCCTCCAAGTACTACAAAGCCATTGAGGGCAAGTACTGCTT
CACCATGCAATAGTAACATAAATGCAGCTACAGCTGTGGCTCTACAGGAACCCCGAAAGTTAGGTTATGCTGAAGTTTGC
CAGAAGCCCCCTAAAGAGCCATCTTCAGTTCTTGTGTAGCCACTATGGGAACTTCGCTCCAATGTAGTGTCTCCCACCAA
AAACGAAGACAGTGAAGCTCCTGAGAAGTCCCTTGAGAAACCACATGAGAAGTTAGAAGCAAGGGCTAGTAAGGATTATT
CTGGCTTCTGAGGCAATACCATTCCCAGGGGAGCAGATGGAAAAATCAGGGAACAGAGATGCCAGTTTAGTCATAGGGCT
ATACCTCAGGGAGTGACACGACGTAATGGCAAAGAGCAATATGTGCCACCCAGATCACCAAAG

Alignment

ORF - retro_mmul_2129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFFAKNGYRLMDSSIYSQPIQTQAQYASPVFMQPVYNPHQQYSVYSIVPQSWSPNPTPYFETPLAPFPNG
          TFFAKNG...MDSSIYSQPIQTQAQYASP.F.QPVYNPHQQ.SVYSIVPQ.WSPNPTPYFETPLAPFPNG
Retrocopy TFFAKNGH**MDSSIYSQPIQTQAQYASPDFRQPVYNPHQQCSVYSIVPQFWSPNPTPYFETPLAPFPNG

Parental  SFVNGFNSPGSYKTNAAAMNMGRPFQK-NRVKPHFRSSSGSEHSTEGSVSLGDGQL-NRSSSRNLPTERH
          SFVNGFNSPGSYKTNAAAMNMGRPFQK....KPHFRSSSGSEHSTE.SVSLGDGQL...SS....P.E.H
Retrocopy SFVNGFNSPGSYKTNAAAMNMGRPFQK>YLAKPHFRSSSGSEHSTEDSVSLGDGQL>RSSSRNFSP-EQH

Parental  NPTVTGHQEQTYLQKETSTLQMEQNGDYGRGRRTLFRGRRRREDDRISRSHPSTAESKAPTPKFDLLASN
          NPTVTG..EQT.LQKETSTLQMEQNGDYGRG.RTLFRGRRR..DDRISR.HPST.ESKAPTPKFDLLASN
Retrocopy NPTVTGD*EQT*LQKETSTLQMEQNGDYGRG-RTLFRGRRR*QDDRISRPHPSTVESKAPTPKFDLLASN

Parental  FPPLPGSSSRMPGELILENRMSDVVKGVYKEKDNEELRVSCPVPADEQTECTSAQQLNMSSSSPCAAELT
          FPPLPGSSS..PG.LI.ENRMSDVVKG.YKEKDNEELRV.CPVPADEQTECTSAQQL.MS.SS.CAAELT
Retrocopy FPPLPGSSSSIPGKLISENRMSDVVKGIYKEKDNEELRVGCPVPADEQTECTSAQQLSMSTSSSCAAELT

Parental  ALSTTQQEKDLIEDSSVQKDGLNQTTMPVSPPSTTKPSRASTASPCNNNINAAIAVALQEPRKLSYAEVC
          ALSTTQQ.KDLIEDSSVQKD..NQTT.PVSPPSTTKP.RASTASPCN.NINAA.AVALQEPRKL.YAEVC
Retrocopy ALSTTQQKKDLIEDSSVQKDCPNQTTIPVSPPSTTKPLRASTASPCNSNINAATAVALQEPRKLGYAEVC

Parental  QKPPKEPSSVLVQPLRELRSNVVSPTKNEDSGAPENSVEKPHEKPEARASKDYSGFRGNTIPRGAAGKIR
          QKPPKEPSSVLV.PL.ELRSNVVSPTKNEDS.APE.S.EKPHEK.EARASKDYSGF.GNTIPRGA.GKIR
Retrocopy QKPPKEPSSVLV*PLWELRSNVVSPTKNEDSEAPEKSLEKPHEKLEARASKDYSGF*GNTIPRGADGKIR

Parental  EQRRQFSHRAIPQGVTRRNGKEQYVPPRSPK
          EQR.QFSHRAIPQGVTRRNGKEQYVPPRSPK
Retrocopy EQRCQFSHRAIPQGVTRRNGKEQYVPPRSPK

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	30.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.58 RPM
SRP007412_cerebellum	0.19 RPM	36.81 RPM
SRP007412_heart	0.18 RPM	21.96 RPM
SRP007412_kidney	0.00 RPM	43.07 RPM
SRP007412_liver	0.00 RPM	29.96 RPM
SRP007412_testis	0.15 RPM	21.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2129 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2129 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000161813	1 retrocopy	retro_hsap_1483,
Myotis lucifugus	ENSMLUG00000012513	1 retrocopy	retro_mluc_1180,
Macaca mulatta	ENSMMUG00000008172	1 retrocopy	retro_mmul_2129 ,
Mus musculus	ENSMUSG00000023025	1 retrocopy	retro_mmus_3568,
Nomascus leucogenys	ENSNLEG00000017798	1 retrocopy	retro_nleu_2388,
Pan troglodytes	ENSPTRG00000004935	1 retrocopy	retro_ptro_1003,
Rattus norvegicus	ENSRNOG00000049091	1 retrocopy	retro_rnor_644,