RetrogeneDB ID: retro_mmul_1432

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:48805533..48805937(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2291
• Ensembl ID: ENSMMUG00000019630
• Aliases: None
• Description: glutathione S-transferase mu 2 (muscle) [Source:RefSeq peptide;Acc:NP_001248580]

Sequence

>retro_mmul_1432
GCCCGCAAGCACAACTTGTGTGGGGAGACAGAAGAGGAGAAGATTCGTGTGGACATTTTGGAGAACCAGTCCATGGACAA
CCTGATGCAGCTGGCCATGATCTGCTACATCCCAGAATTTGAGAAAGTGAAGCCAAAGTACTTGGAGGAACTCCCTGAAA
AGCTAACGCTCTACTCGCAGTTTCTGGGGAAGCGGCCATGGTTTGCAGGAGACGAAATCACCTTTGTGGACTTCCTTGCC
TATGACATCCTTGACCTGAACTGTATATTTGAGCCCAGCTGCCTGGATGTCTTCCCAAACCTGAAGGACTTCATCTCCCG
ATTTGAGGGTTTGAAAAGATCTCTGCCTACATGAAGTCCAGCCTCCAAGGTCCTTTGTTTGGGAGGTCAGCTATGCCTGG
GAGC

Alignment

ORF - retro_mmul_1432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARKHNLCGETEKEKIREDILENQLMDNRMQLARLCYDPDFEKLKPEYLEGLPEMLKLYSQFLGKQPWFLG
          ARKHNLCGETE.EKIR.DILENQ.MDN.MQLA..CY.P.FEK.KP.YLE.LPE.L.LYSQFLGK.PWF.G
Retrocopy ARKHNLCGETEEEKIRVDILENQSMDNLMQLAMICYIPEFEKVKPKYLEELPEKLTLYSQFLGKRPWFAG

Parental  DKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGL-EKISAYMKSSRFLPRPVFTKMAVWGN
          D.ITFVDF.AYD.L..N..FEPSCLD.FPNLKDFISRFEGL.EKISAYMKSS..L..P.F...A..G.
Retrocopy DEITFVDFLAYDILDLNCIFEPSCLDVFPNLKDFISRFEGL<EKISAYMKSS--LQGPLFGRSAMPGS

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	141.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	94.32 RPM
SRP007412_cerebellum	0.00 RPM	167.89 RPM
SRP007412_heart	0.00 RPM	234.78 RPM
SRP007412_kidney	0.12 RPM	137.20 RPM
SRP007412_liver	0.00 RPM	2033.54 RPM
SRP007412_testis	0.04 RPM	147.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1432 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1432 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2751
Pan troglodytes	retro_ptro_1859
Gorilla gorilla	retro_ggor_1913
Pongo abelii	retro_pabe_2218

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432 , retro_mmul_1806,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,