RetrogeneDB ID: retro_mmul_771

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099548049727:83514..84221(+)
• Located in intron of: ENSMMUG00000016712

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12926
• Ensembl ID: ENSMMUG00000015152
• Aliases: None
• Description: splicing factor 45 [Source:RefSeq peptide;Acc:NP_001244661]

Sequence

>retro_mmul_771
GACCTGCAAATTGGGGACACACCACAGCATGCAGCAGCTGGGCTGAAGGATGCTGTTCCCAGTGGGTTTCTGCAGGGGAC
GTTCTGATTCCCTTAACTGACGAATATGATCCTAGGTTTCCTTATGATTATGAGAAAGTAATGAAGCGCCAAAGAGAGGA
ATGACAGACACAGCAGGAGCTAGAAATACGAAAGGAAATAGAAGAAAGGGAAAAGAGGCCTAAAAACAGGCAGAAAGCTA
GGGGGGTTCTGATCAAGGTGACTCAGATCCAGATTCTGATGAAGATGAAGATTAGGAGTGAGAGAGGAGGAAAAGAAGTA
GGGCGGAGCTGCCATTGCCCCACCCACTTTTCTGGTAGAGAAAGAGTCACCCCGAGATTTTCCTTATGAAGAGGATTCAA
GACCTCAATCACGGGCTTCCAAAGCTGCCATTCCTCCCCTAGTGAAGGAGGAACAGGACAGACCGAGATCTCCAAACCGG
CCTAGTAGCTCCTTCCTCGCTAACGTGGTGGGAACGGTGGCGCACAACCTCATGCAGAAGCGCGGCTTCCGGGAAGGCTA
GGGCCTCAGGGAGCACCAGCAGAGGCTGCGCGCCACCTTTCCGGTGGGGAAGACCAGCAAACCTGGCGGCAAGATCATCA
TGGGCGATGCCGCGGAGAAAGATGCAGTGAAGAATCAGGTACAAATCCACTGACTGAAATAATTGAG

Alignment

ORF - retro_mmul_771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.96 %
• Parental protein coverage: 59.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DRQIVDTPPHVAAGLKDPVPSGF-SAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEE
          D.QI.DTP.H.AAGLKD.VPSGF.SAG.VLIPL.DEYDP.FP.DYEKV.KRQREE.Q.Q.ELE..KEIEE
Retrocopy DLQIGDTPQHAAAGLKDAVPSGF<SAGDVLIPLTDEYDPRFPYDYEKVMKRQREE*QTQQELEIRKEIEE

Parental  REKRRKDRHEASGF-ARRPDPDSD--EDEDYERERRKRSM-GGAAIAPPTSLVEKDKELPRDFPYEEDSR
          REKR.K.R..A.G......D.D.D..EDED.E.ERRKRS..GGAAIAPPT.LVE..KE.PRDFPYEEDSR
Retrocopy REKRPKNRQKARGV<SDQGDSDPDSDEDED*E*ERRKRSR<GGAAIAPPTFLVE--KESPRDFPYEEDSR

Parental  PRSQSSKAAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEK
          P.S..SKAAIPP.V.EEQDRPRSP..PS.SFLAN..GTVAH..MQK.GFREG.GL..H.Q.L.....V.K
Retrocopy PQSRASKAAIPPLVKEEQDRPRSPNRPSSSFLANVVGTVAHNLMQKRGFREG*GLREHQQRLRATFPVGK

Parental  TSKRGGKIIVGDATEKDA-SKKSDSNPLTEILK
          TSK.GGKII.GDA.EKDA.S..S..NPLTEI..
Retrocopy TSKPGGKIIMGDAAEKDA<SEESGTNPLTEIIE

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	43.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	32.45 RPM
SRP007412_cerebellum	0.00 RPM	60.12 RPM
SRP007412_heart	0.00 RPM	33.09 RPM
SRP007412_kidney	0.12 RPM	40.61 RPM
SRP007412_liver	0.00 RPM	19.59 RPM
SRP007412_testis	0.57 RPM	56.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_771 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_771 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771 ,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,