RetrogeneDB ID: retro_mmul_383

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:80928339..80928882(+)
• Located in intron of: ENSMMUG00000002904

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSMMUG00000016970
• Aliases: None
• Description: translocon-associated protein subunit gamma [Source:RefSeq peptide;Acc:NP_001253473]

Sequence

>retro_mmul_383
ATAGCTCCCAAAGGCAGCTCCAAACAGTCGTCCAAGGAGGACCTGCTCCTGCAGGATTTCAGTGGCAACCTCTCTGCCAA
GTCCTTTGTGATCTTTTTCAGGAATGCTTTCGTCGTGTCTGCCATCCGAATCTGGTTATACTGGAGAATATGGCATATGG
ATCTTATTCAGTCTGCTGTTTTCCATAGTGTGATGACCCTAGAAAGTACATATTTGGTAGCCTTTGCATACAAGAATGTG
AAATTTGTTCTCAAGCACAAAGTAGCACAGCAGAGGGAGGATGCAGTGATTCGAAAACTTTCTGAAGCTGATAATAGAAA
GATGTCTCGGAAAGAGAAAGATGTAAGAATCTTGTGGAAGAAAGAATGACGTTGCTGATTCTGAAGCTACAACATTTTCC
ATCTTCTATAACAACACTCTGTTCCTGGTCTTGGTCATTGTTGCTTCTTCTTCATATTGAAGAATTTCAACCCCACAATG
AACTACATTTTGTCCCTAAGTGCTTCATCAGGACTCAATGCCCTCCTGTCTACTGGCTCCAAG

Alignment

ORF - retro_mmul_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVST
          .APKGSSKQ.S.EDLLLQDFS.NLSAKS...FF.NAF.VSAI.IWLYWRIWHMDLIQSAV..SVMTL.ST
Retrocopy IAPKGSSKQSSKEDLLLQDFSGNLSAKSFVIFFRNAFVVSAIRIWLYWRIWHMDLIQSAVFHSVMTLEST

Parental  YLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWK-KNEVADYEATTFSIF
          YLVAFAYKNVKFVLKHKVAQ.REDAV.....RKLSEADNRKMSRKEKD.RILWK.KN.VAD.EATTFSIF
Retrocopy YLVAFAYKNVKFVLKHKVAQQREDAV----IRKLSEADNRKMSRKEKDVRILWK>KNDVADSEATTFSIF

Parental  YNNTLFLVVVIVAS-FFILKNFNPTVNYILSISASSGLIALLSTGSK
          YNNTLFLV.VIVAS.FFILKNFNPT.NYILS.SASSGL.ALLSTGSK
Retrocopy YNNTLFLVLVIVAS<FFILKNFNPTMNYILSLSASSGLNALLSTGSK

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	31.93 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.80 RPM
SRP007412_cerebellum	0.00 RPM	36.42 RPM
SRP007412_heart	0.00 RPM	52.58 RPM
SRP007412_kidney	0.47 RPM	86.62 RPM
SRP007412_liver	0.00 RPM	62.11 RPM
SRP007412_testis	0.08 RPM	34.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_383 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_383 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_173
Pan troglodytes	retro_ptro_163
Gorilla gorilla	retro_ggor_255
Pongo abelii	retro_pabe_456

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059, retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243, retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383 ,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660,