RetrogeneDB ID: retro_mmul_787

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:8771767..8772930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2327
• Ensembl ID: ENSMMUG00000004380
• Aliases: None
• Description: trifunctional enzyme subunit alpha, mitochondrial [Source:RefSeq peptide;Acc:NP_001252819]

Sequence

>retro_mmul_787
TCTTCCGCTTTGCTGACCAGAACCCATATGAACCACGGAGTCAAAGGGGATGTGGCAATTATTCGAATTAACTCTCCCAA
TTCAAAAGTAAATACACTGAATGAAGAGCTGCATTCAGAGTTCACAGAAGTTATGAATGAAATCTGGGTTACTAATCACA
TCAGAAGTGCCGCCCTTATCTCATCAAAGCCAGGCTGCTTTATTGCAGGTGCTCATATCAACATGTTAGCCACTTGCAAG
ACCCCTCAAGAAGTAACACAGATGTCACAAGAAGCATAGAGAACATTTGAGAAACTTGAGAAGGTCACAAAGCCTGTTTG
ATCCATCAATGGATCCTGCCTGGGAGGAGGACTTGAGCTTGCCATTTCATGCCAATACAGAATAGCAACAAAAGACGGAA
AAACATATTAGGTGCCCCTGAAGTCTTGCTGGGGCTCTTACCAGGAGCAGGAGGCACACAAAGGTTGCCCAAAATGGTGG
GTGTGCCTGCTGCTTTTGACATGATGCTGCCTAGTAGAAACATTCATGCAGACAGGGCAAAGAAAATGGGACTGGTTGAC
CGATTGGTGGAACCCCTGGGAACAGGACTAAAACCTCCAGAGTAACGGGCAATAGAATACCAAGAAGAAGTTGCCATTAC
TTTCGCCAAAGGTCTAGCTGATAAGATCTCTCCAAAGAGAGACAAGGGATTGGTGGAAAAATTGACAGGATACGCCATGA
CCATTCCATTTGTCAGGCAACAGGTTTCCAAAAAAGTAGAAGAAAAAGTGCGAAAGGAGACTAAAGGTCTTTATCCTGCG
CCTCTGAAAATAATTGATGTGGTAAAGACTGGAATTGAGCAAGGGAGTGATGCTGGTTATCTCTCTGAATCTCAGAAATT
TGGAGAGCTTGCAATGACCAGTGAATCAAAGGCCTTGATGGGATTCTGCCATGGTCAGGTCTTGTGCAAGAAGAATAAAT
TTGGAGCTCCACAGAAGGATGTGAAGCATCTGGTTATTCTTGGTGAAGGGCTGAAGGGAGCAGACATTGCCCAAGTCTCT
GTGGATAAGAGGCTAAAGACTATACTTAAAGATGCCACACTCACTAGGCTAGGCCAAGGACAGCAACAAGTGTTCAAAGG
ATTGAATGATAAAGTGAAGAAGAAAGCTCTAACATCATTTGAA

Alignment

ORF - retro_mmul_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.68 %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSALLTRTHINYGVKGDVAVVRINSPNSKVNTLSKELHSEFTEVMNEIWASDQIRSAVLISSKPGCFIAG
          SSALLTRTH.N.GVKGDVA..RINSPNSKVNTL..ELHSEFTEVMNEIW....IRSA.LISSKPGCFIAG
Retrocopy SSALLTRTHMNHGVKGDVAIIRINSPNSKVNTLNEELHSEFTEVMNEIWVTNHIRSAALISSKPGCFIAG

Parental  ADINMLSACKTLQEVTQLSQEAQRILEKLEKSPKPVVAAINGSCLGGGLELAISCQYRIATKD-RKTVLG
          A.INML..CKT.QEVTQ.SQEA.R..EKLEK..KPV...INGSCLGGGLELAISCQYRIATKD.RK..LG
Retrocopy AHINMLATCKTPQEVTQMSQEA*RTFEKLEKVTKPV*S-INGSCLGGGLELAISCQYRIATKD<RKNILG

Parental  VPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRNIRADRAKKMGLVDQLVEPLGPGLKPPEERTMEYL
          .PEVLLG.LPGAGGTQRLPKMVGVPAA.DMML..RNI.ADRAKKMGLVD.LVEPLG.GLKPPE.R..EY.
Retrocopy APEVLLGLLPGAGGTQRLPKMVGVPAAFDMMLPSRNIHADRAKKMGLVDRLVEPLGTGLKPPE*RAIEYQ

Parental  EEVAITFAKGLADKKISPKRNKGLVEKLTAYAMTIPFVRQQVYKKVEEKVRKQTKGLYPAPLKIIDVVKT
          EEVAITFAKGLADK.ISPKR.KGLVEKLT.YAMTIPFVRQQV.KKVEEKVRK.TKGLYPAPLKIIDVVKT
Retrocopy EEVAITFAKGLADK-ISPKRDKGLVEKLTGYAMTIPFVRQQVSKKVEEKVRKETKGLYPAPLKIIDVVKT

Parental  GIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLCKKNKFGAPQKDVKHLAILGAGLMGAGIAQVS
          GIEQGSDAGYLSESQKFGEL.MT.ESKALMG..HGQVLCKKNKFGAPQKDVKHL.ILG.GL.GA.IAQVS
Retrocopy GIEQGSDAGYLSESQKFGELAMTSESKALMGFCHGQVLCKKNKFGAPQKDVKHLVILGEGLKGADIAQVS

Parental  VDKGLKTILKDATLTGLDRGQQQVFKGLNDKVKKKALTSFE
          VDK.LKTILKDATLT.L..GQQQVFKGLNDKVKKKALTSFE
Retrocopy VDKRLKTILKDATLTRLGQGQQQVFKGLNDKVKKKALTSFE

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	55.02 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	55.85 RPM
SRP007412_cerebellum	0.00 RPM	61.67 RPM
SRP007412_heart	0.00 RPM	306.62 RPM
SRP007412_kidney	0.00 RPM	191.31 RPM
SRP007412_liver	0.00 RPM	102.13 RPM
SRP007412_testis	0.00 RPM	178.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_787 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_787 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_958
Pan troglodytes	retro_ptro_664
Gorilla gorilla	retro_ggor_772

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787 ,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,