RetrogeneDB ID: retro_mmul_1209

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:110002295..110003006(-)
• Located in intron of: None

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_1209
GATGACCTGCAAATTGGGGACACACCACGGCATGCAGCAGCTGGGCTGAAGGATGCTGTTCCCAGTGGGTTTCTGCAGGG
GACGTTCTGATTCTCTTAGCTGACGAATATGATCCTAGGTTTCCTTATGATTACGAGAAAGTAATGAAGCGCCAAAGAGA
GGAATGACAGACACAGCAGGAGCTAGAAATACGAAAGGAAATAGGAGAAAGGGAAAAGAGGCCTAAAGACAGGCAGAAAG
CTAGGGGGGTTCTGATCAAGGCGACCAGATCCAGATTCTGATGAAGACAAAGATTAGGAAAGAGAGGAGGAAAAGAAGTA
GGGCGGAGCTGCCATTGCCCCACCTACTTTTCTGGTAGAGAAAGACAAGAGTCACCCCGAGATTTTCCTTATGAAGAGGA
TTCAAGACCTCAGGCACGGTCTTCCAAAGCTGCCAATCCTCCCCCAGTGGAGGAGGAACAGGACAGACCGAGATCTCCAA
ACAGCCTAGTAGCTCCTTCCTCGCTAACGTGGTGGGAACGGTGGCGCAAAACATCATGCAGAAGCGCGGCTTCCGGGAAG
GCTAGGGCCTCAGGGAGCACCAGCAGAGGCTGCGCGCCGCCTTTCCGGTGGGGAAGACCAGCAAACCTGGCGGCAAGATC
ATCATGGGCGACGCCGCGGAGAAAGATGCAGTGAAGAATCAGGTACAAATCCACTGACTGAAATACTCGAG

Alignment

ORF - retro_mmul_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.85 %
• Parental protein coverage: 59.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DDRQIVDTPPHVAAGLKDPVPSGF-SAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIE
          DD.QI.DTP.H.AAGLKD.VPSGF.SAG.VLI.LADEYDP.FP.DYEKV.KRQREE.Q.Q.ELE..KEI.
Retrocopy DDLQIGDTPRHAAAGLKDAVPSGF<SAGDVLILLADEYDPRFPYDYEKVMKRQREE*QTQQELEIRKEIG

Parental  EREKRRKDRHEA-SGFARRPDPDSDEDE-DYERERRKRSMGGAAIAPPTSLVEKDK-ELPRDFPYEEDSR
          EREKR.KDR..A..GF..R..........D.ERE..K...GGAAIAPPT.LVEKDK.E.PRDFPYEEDSR
Retrocopy EREKRPKDRQKA>GGF*SRRPDPDSDEDKD*EREEEKK-*GGAAIAPPTFLVEKDK<ESPRDFPYEEDSR

Parental  PRSQSSKAAIPPPVYEEQDRPRSPTG-PSNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVE
          P...SSKAA.PPPV.EEQDRPRSP...PS.SFLAN..GTVA..IMQK.GFREG.GL..H.Q.L..A..V.
Retrocopy PQARSSKAANPPPVEEEQDRPRSPNS<PSSSFLANVVGTVAQNIMQKRGFREG*GLREHQQRLRAAFPVG

Parental  KTSKRGGKIIVGDATEKDA-SKKSDSNPLTEILK
          KTSK.GGKII.GDA.EKDA.S..S..NPLTEIL.
Retrocopy KTSKPGGKIIMGDAAEKDA<SEESGTNPLTEILE

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	0.39 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	0.90 RPM	56.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1209 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1209 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,