RetrogeneDB ID: retro_mmul_988

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:54774621..54775071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15H9orf85
• Ensembl ID: ENSMMUG00000018881
• Aliases: None
• Description: None

Sequence

>retro_mmul_988
AGCTCCCAGAAAGGTGCAGCGTGGCTCATTCCAGGCCTCAAGCACCAGAATACGTTTAGCTTCAAAAATGACAAGTTCGA
TAAGAGTGTTCAGACCAAGGAAATTAATGCAAAATTTCCTGATGGAGTATGTCAGCGCTATAAAGAAGTTCTTGAGTGTT
GTGTAAAATACAAAAAATATATGAACCATTATCAAAACCTAAAAAATGTGTTAAATGTTTATAAAAGACAGTGAAGGATT
CTTACTACACAATATGTAGACCATGCGCCTGTGAACTTGAAGTTTGCACAAAATGTGGAAAGAAGAGATTGTTATTCCGT
TCAACAAGGAACCAGAAAAAAGCAAAATATTGAAAACAATCTAAGTTCCAACCATAGAAGAAGCTGCAGAAGAAATGAAG
AAAGGGATGATAATTTAGATTTTGATGTTGATTTTGAAGACACAGGAGGA

Alignment

ORF - retro_mmul_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.55 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSQKGNVARSRPQKHQNTFSFKNDKFDKSVQTKKINAKLHDGVCQRCKEVLEWRV-KYSK-YKPLTKPKK
          SSQKG........KHQNTFSFKNDKFDKSVQTK.INAK..DGVCQR.KEVLE..V.K..K.Y.PL.KPKK
Retrocopy SSQKGAAWLIPGLKHQNTFSFKNDKFDKSVQTKEINAKFPDGVCQRYKEVLECCV<KIQKIYEPLSKPKK

Parental  CVKCLQKTVKDSYHIMCRPCACELEVCAKCGKK-EDIVIPLNKE-TEKIEHTENNLSSNHRRSCRRNEES
          CVKCL.KTVKDSY...CRPCACELEVC.KCGKK.E....P.NKE.T.K....ENNLSSNHRRSCRRNEE.
Retrocopy CVKCL*KTVKDSYYTICRPCACELEVCTKCGKK<EIVI-PFNKE<TRKKQNIENNLSSNHRRSCRRNEER

Parental  DDDLDFDIDLEDTGG
          DD.LDFD.D.EDTGG
Retrocopy DDNLDFDVDFEDTGG

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	0.34 RPM	0.78 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	0.79 RPM
SRP007412_cerebellum	0.39 RPM	0.84 RPM
SRP007412_heart	0.29 RPM	1.53 RPM
SRP007412_kidney	0.35 RPM	1.64 RPM
SRP007412_liver	0.00 RPM	0.48 RPM
SRP007412_testis	0.00 RPM	11.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_988 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_988 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2104
Pan troglodytes	retro_ptro_1543
Pongo abelii	retro_pabe_1996
Callithrix jacchus	retro_cjac_1283

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988 ,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996, retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,