RetrogeneDB ID: retro_mmul_2405

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:61627479..61627916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3661
• Ensembl ID: ENSMMUG00000008480
• Aliases: None
• Description: sperm autoantigenic protein 17 [Source:RefSeq peptide;Acc:NP_001165553]

Sequence

>retro_mmul_2405
ATGTCGATTCCATTCTCCAACACCCACTACTGAATTCTGCAAGGATTTGGGAGTCTTCTTGAAGGGCTGACACACGAGAT
TCTGAGAGAGCAGCTGGATAATATACAGCTTTTGCAGCAGCATATTTTGAGAGCTTTCTAGAGAATAGAGAGAAAACCAC
TTTTGATCCAGCAGAATGGGGGACTCAGGTAGAAGACCGCTTCTAGAACAGCCATGCATTCGAGGAGCAAGAACCACCTG
AGAAATGTGATCCTAAACAAGAAAACTCCCCGATATCTGGGAAGGAGGAAGAGACACCAGTCACCATCTTAGACTCTTCT
GAGGAAGATAAGGAAAAAGAAGAGGTTGCTGCTGTCAAAATCCAAGCTGCCTTCTGGGGACACATAGCCAGAGAGGAGGT
AAGGAGAATGGAAACAGATAGTCTCCAACTTGAGGAA

Alignment

ORF - retro_mmul_2405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIPFSNTHYRIPQGFGNLLEGLTREILREQPDNIP-AFAAAYFESLLEKREKTNFDPAEWGSKVEDRFY
          MSIPFSNTHY.I.QGFG.LLEGLT.EILREQ.DNI..AFAAAYFES.LE.REKT.FDPAEWG..VEDRF.
Retrocopy MSIPFSNTHY*ILQGFGSLLEGLTHEILREQLDNIQ<AFAAAYFESFLENREKTTFDPAEWGTQVEDRF*

Parental  NNHAFEEQEPPEKSDPKQEESQIPGKEEEASVTILDSSEEDKEKEEVAAVKIQAAFRGHVAREEVKKMKT
          N.HAFEEQEPPEK.DPKQE.S.I.GKEEE..VTILDSSEEDKEKEEVAAVKIQAAF.GH.AREEV..M.T
Retrocopy NSHAFEEQEPPEKCDPKQENSPISGKEEETPVTILDSSEEDKEKEEVAAVKIQAAFWGHIAREEVRRMET

Parental  DSLQNEE
          DSLQ.EE
Retrocopy DSLQLEE

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	3.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.06 RPM
SRP007412_cerebellum	0.00 RPM	0.71 RPM
SRP007412_heart	0.00 RPM	0.65 RPM
SRP007412_kidney	0.00 RPM	2.11 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.26 RPM	231.17 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2405 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2405 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_696
Pan troglodytes	retro_ptro_500
Gorilla gorilla	retro_ggor_593
Pongo abelii	retro_pabe_529
Callithrix jacchus	retro_cjac_978

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007961	1 retrocopy	retro_cjac_978,
Echinops telfairi	ENSETEG00000007789	1 retrocopy	retro_etel_911,
Homo sapiens	ENSG00000064199	1 retrocopy	retro_hsap_696,
Gorilla gorilla	ENSGGOG00000003757	1 retrocopy	retro_ggor_593,
Macaca mulatta	ENSMMUG00000008480	1 retrocopy	retro_mmul_2405 ,
Nomascus leucogenys	ENSNLEG00000007436	1 retrocopy	retro_nleu_2229,
Pongo abelii	ENSPPYG00000004017	1 retrocopy	retro_pabe_529,
Pan troglodytes	ENSPTRG00000004426	1 retrocopy	retro_ptro_500,
Tarsius syrichta	ENSTSYG00000008379	1 retrocopy	retro_tsyr_2091,