RetrogeneDB ID: retro_mmul_2475

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:15660452..15661201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM4
• Ensembl ID: ENSMMUG00000011236
• Aliases: None
• Description: None

Sequence

>retro_mmul_2475
TGGAATGAGTCAATACTGGAGCAGATAGGTGTTGCAATAAAAGTAGGAGCTACTGCTACTGATAAAACAAGCAAAAAAGT
AGGGAATGTGAGCAACAAAAATGTGATTGATGTAGGAAAAATGAACTTGAGGACTCTCCACCCTTAAAAGATTACACTGA
TATTGAAGTTACTTCTGAGGATGTGTGGTAGTGTTACTGAGTGTAAGAAATTTAACTTTCCAAACAGGAGATGTTTCTGT
TGCAAGGCCTTGAGGAACGATTGGTATTCAGACTCTTCTAAGTTAACCCATTCTCTCTTCATGCCTGTTATCACTGCTGT
ACCCCACAAAACAAGGAAAATGAAGGAAAAAGAAAATAATGTCTCAGATCACCAAAGAACCATTACAGTTCCAGTTGTTA
CAGCCAAAGATCTATATGTAAAGGAAGAAAAAGTCCAACTTCTTCCCTGCAGCTCAGCACATTTCTCGGATTTGGCTCAC
AGTTCTGAAAGCCTAGAAGCCATCTCAAGCTCAGGACAACAATCAGATATCCTTTCAGACCAGAGAGCAGATACAGAATG
CATGGAGGACTGGCAAAACCTCTGGAGGTCATTCGGTATATGTGAGAAAAGACCAGGAGACAGAAATATTATTCATGGAA
GGACAGGCCATCTTGTCATTTATTTTCACTGTGCCAGAAGATTAAAGAAGTCTGGTTTTCATGCCTCCTTTGCAAGAAGA
TTCAACTGGTTATTAAGGTTTTTATGGCA

Alignment

ORF - retro_mmul_2475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.48 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FERSVSEQLGVGIKVEAGDTEQTSEEVGKVSDKKVIEMG-KNDDLEDSKSLSDDTDVEVTSEDEWQC-TE
          ...S..EQ.GV.IKV.A..T..TS..VG.VS.K.VI..G.KN..LEDS..L.D.TD.EVTSED.W.C.TE
Retrocopy WNESILEQIGVAIKVGATATDKTSKKVGNVSNKNVIDVG<KNE-LEDSPPLKDYTDIEVTSEDVW*C>TE

Parental  CKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSLSTSDITAIPEK----ENEGNDVPDCRRTISAPVVRPK
          CKKFN.P..R.CF.C.ALR.DWYSD.SKLTHSL....ITA.P.K........N.V.D..RTI..PVV..K
Retrocopy CKKFNFPNRR-CFCCKALRNDWYSDSSKLTHSLFMPVITAVPHKTRKMKEKENNVSDHQRTITVPVVTAK

Parental  DVYIKKENSKLFDPCNSVEFLDLAHSSESQETISSTGEQLDNLSEQRTDTENMEDCQNLLKPCSLCEKRP
          D.Y.K.E...L..PC.S..F.DLAHSSES.E.ISS.G.Q.D.LS.QR.DTE.MED.QNL......CEKRP
Retrocopy DLYVKEEKVQLL-PCSSAHFSDLAHSSESLEAISSSGQQSDILSDQRADTECMEDWQNLWRSFGICEKRP

Parental  RDGNIIHGRTGHLVTCFHCARRLKKAG-ASCPICKKEIQLVIKVFIA
          .D.NIIHGRTGHLV..FHCARRLKK.G..SC..CKK.IQLVIKVF.A
Retrocopy GDRNIIHGRTGHLVIYFHCARRLKKSG<FSCLLCKK-IQLVIKVFMA

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	12.77 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.66 RPM
SRP007412_cerebellum	0.00 RPM	22.41 RPM
SRP007412_heart	0.00 RPM	4.48 RPM
SRP007412_kidney	0.00 RPM	10.09 RPM
SRP007412_liver	0.00 RPM	4.43 RPM
SRP007412_testis	0.00 RPM	32.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2475 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001126	1 retrocopy	retro_amel_1730,
Macaca mulatta	ENSMMUG00000011236	1 retrocopy	retro_mmul_2475 ,