RetrogeneDB ID: retro_mmul_476

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:30379364..30379944(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17236
• Ensembl ID: ENSMMUG00000014909
• Aliases: None
• Description: charged multivesicular body protein 1a [Source:RefSeq peptide;Acc:NP_001078827]

Sequence

>retro_mmul_476
GACGATACCCTGTTCCAGTTGAAATTTATGGTGAAGCAGCTGGAGAAACCAGACAAGAAGGCAGAAAAGCACTCCTAGGC
CAACCAGGCCAAAGTGAAGAAGTCCCTTCAGCAGAAAAACATAGAGTACACCGTGTGTACGCCAATAACACCATCTGCAA
GGAGAACAGCAGCATGAACTGGCTCCGCGTGGCATCCGCCTGGACACAGTGGCCCCCGAGGTGCAGACAGCTGTGACCAT
GAAGGCGGTGACCAAGAACATGGTGTAGATGACCAAAGCCCCAGACAAGGCCCTGAACACCACGGAGCTGAAGAAGGCCT
CTGCAGCGATGGACAGTTTCGAGCAGCAAGTGTGAAACCTGGCCATGCACATGTTAGTGATGGAGGATTTCATGAGCTCG
GCCACCACACTGACCATGCCTCAGGAGCAAGTGGACAGCCCCATTGTGCAAAACGCCAAGGAGAATGGCCTGGAGGTCCT
AGACCAGCTCAGCCAGTTGCCCAAGGCTGCCTCTGCCTCTGAGAGCTCCGTGTGAAGCCTGGAGGAACAGCTGTCAAGGG
CGCTGGCTGCCCTGAGGAAT

Alignment

ORF - retro_mmul_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.07 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALQQKNVECA-RVYAENAIRKKNEGVNWLRMAS-RV
          DDTLFQLKF..KQLEK..KKAEK.S.A.QAKVKK.LQQKN.E...RVYA.N.I.K.N...NWLR.AS.R.
Retrocopy DDTLFQLKFMVKQLEKPDKKAEKHS*ANQAKVKKSLQQKNIEYT<RVYANNTICKENSSMNWLRVAS<RL

Parental  DAVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTL
          D.VA..VQTAVTMK.VTKNM...TKA.DKAL.T..L.K.S..MD.FEQQV.NL..H..VMED.MSSATTL
Retrocopy DTVAPEVQTAVTMKAVTKNMV*MTKAPDKALNTTELKKASAAMDSFEQQV*NLAMHMLVMEDFMSSATTL

Parental  TTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          T.PQEQVDS.I.Q.A.ENGLEVLDQLSQLP..ASA..ESSV.S.E.QLSR.LAALRN
Retrocopy TMPQEQVDSPIVQNAKENGLEVLDQLSQLPKAASA-SESSV*SLEEQLSRALAALRN

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	4.93 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.50 RPM
SRP007412_cerebellum	0.00 RPM	4.84 RPM
SRP007412_heart	0.00 RPM	5.71 RPM
SRP007412_kidney	0.00 RPM	11.27 RPM
SRP007412_liver	0.00 RPM	24.03 RPM
SRP007412_testis	0.00 RPM	14.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_476 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_476 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_359
Pan troglodytes	retro_ptro_283
Pongo abelii	retro_pabe_344

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476 , retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,