RetrogeneDB ID: retro_mmul_610

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:54799223..54799619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2372
• Ensembl ID: ENSMMUG00000008029
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:RefSeq peptide;Acc:NP_001248509]

Sequence

>retro_mmul_610
GGTGCGACTGAAGAATGAAAGGTGCCAGGAGACATCAGGGAGGAGCAAATGGTGGCATCCCACCTGCAGCTGAAACAGCT
CCACCATGACCCTGACCATGAAACATGGAAGCCTCCATACTTGGAACCGCAACCTGGGCAGCTGAAACATTTCTCCTTGT
TTCTGAGGAAATCATGGTTTCCAGGGAGAAAGCTCACCTTTTTGGATATTCTTACCTGTGAAGTCTTAGATCAGAACTGT
ATGTTTGAACTCAAGTGCCTGGATGAGTTCCCAAATCTGAGGACTTAATGAACCACATTGCAGCTTTGGAGGAAAGAGCT
GCCCCTGTGCAATCTGTCTGTTCTGCAGGATGCCAGTCAGCAGTGAGATGGACCAGTGGGGACCAAGAGCGTATGC

Alignment

ORF - retro_mmul_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 84.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GETEEEKIRVDIIENQVMDFRTQLIRLCYSSDHEKLKPQYLEELPGQLKQFSVFLGKFSWFAGEKLTFVD
          G.TEE.K...DI.E.Q......QL..L....DHE..KP.YLE..PGQLK.FS.FL.K.SWF.G.KLTF.D
Retrocopy GATEE*KVPGDIREEQMVASHLQLKQLHHDPDHETWKPPYLEPQPGQLKHFSLFLRK-SWFPGRKLTFLD

Parental  FLTYDILDQNRIFEPKCLDEFPNLKA-FMCRFEALEKIAAYIQS-DQFFKMPINNKMAQW-GNKPVC
          .LT...LDQN..FE.KCLDEFPNL....M....ALE..AA..QS...F..MP....M.QW.G.K.VC
Retrocopy ILTCEVLDQNCMFELKCLDEFPNLRT<LMNHIAALEERAAPVQS<CLFCRMPVSSEMDQW<GTKSVC

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	0.11 RPM	45.27 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	41.57 RPM
SRP007412_cerebellum	0.06 RPM	79.43 RPM
SRP007412_heart	0.00 RPM	70.60 RPM
SRP007412_kidney	0.00 RPM	6.10 RPM
SRP007412_liver	0.00 RPM	1.86 RPM
SRP007412_testis	0.26 RPM	817.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_610 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_610 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1393

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610 , retro_mmul_941,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,