RetrogeneDB ID: retro_mmul_1864

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:147892702..147893313(-)
• Located in intron of: ENSMMUG00000014635

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12291
• Ensembl ID: ENSMMUG00000005194
• Aliases: None
• Description: Triosephosphate isomerase [Source:UniProtKB/TrEMBL;Acc:F7CT69]

Sequence

>retro_mmul_1864
CCCCCGCTGCCTATATCGACTTTGCCCCAGAAGCCAGAGCTGAAGATTGCTGTGACTGCGCAGAACTGCTACAAAGTAAC
TAACGGGGCCTTTACTGCGGAGATCACCCCTGGAATGATCAAAGACTGCGAAGCCAGTCTGGGGTCCTGGGGCACTCAGA
GAGTGGCATGTCTTTGGGGAGTCAGATGAGCTGATTGAGCAGAAAGTGACCCATGCTCTGGCAGAGGGACTCAGAGTAAT
CGCTTGCATTGGGGAGAAGCTAGCTGAAAGGGAAGTGGCATCATTGAGAAGTTTGTTTTCGAGCAGAAGAAGGTCATCAC
AGATAATGTGAAGGACTGGAGCAAGGTCATCCCGGCCTATGAGCCCACGTGGGCCATTGGTAGCAGCAAGACTGCATCAC
CCTAGCAGGCCCAGAAAGTACACGAGAAGCTCCAAGAATGGCTTAAGTCCAACGTCTCTGATGCGGTGGCTCAGAGCACC
CGTATCATTTATGGAGGCTCTGTGATGGGGCAAGCTGCAAGGAGCTGGGCAGCCAGCCTGAGGTGGATGGCTTCCTCATG
GGTAATGCTTCCCTCAAGCCCGAATTCGTGGACATCATCAATGCCAATGAG

Alignment

ORF - retro_mmul_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 96.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWV-VLGHSERR-HVFGESDELIGQ
          P...I....QK...KIAV.AQNCYKVTNGAFT.EI.PGMIKDC.A....VLGHSE...HVFGESDELI.Q
Retrocopy PPLPISTLPQKPELKIAVTAQNCYKVTNGAFTAEITPGMIKDCEASLG<VLGHSESG<HVFGESDELIEQ

Parental  KVAHALAEGLGVIACIGEKLDERE-AGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQ
          KV.HALAEGL.VIACIGEKL.ERE..GI.EK.VFEQ.KVI.DNVKDWSKV..AYEP.WAIG..KTA.P.Q
Retrocopy KVTHALAEGLRVIACIGEKLAERE<SGIIEKFVFEQKKVITDNVKDWSKVIPAYEPTWAIGSSKTASP*Q

Parental  AQEVHEKLRGWLKSNVSEAVAQSTRIIYGGSV-TGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          AQ.VHEKL..WLKSNVS.AVAQSTRIIYGGSV..GA.CKEL.SQP.VDGFL.G.ASLKPEFVDIINA..
Retrocopy AQKVHEKLQEWLKSNVSDAVAQSTRIIYGGSV<DGASCKELGSQPEVDGFLMGNASLKPEFVDIINANE

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	228.92 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	528.10 RPM
SRP007412_cerebellum	0.00 RPM	202.83 RPM
SRP007412_heart	0.00 RPM	210.04 RPM
SRP007412_kidney	0.12 RPM	177.23 RPM
SRP007412_liver	0.00 RPM	229.03 RPM
SRP007412_testis	0.11 RPM	216.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1864 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1864 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3510
Pan troglodytes	retro_ptro_2382
Pongo abelii	retro_pabe_2902
Callithrix jacchus	retro_cjac_2370

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864 , retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,