RetrogeneDB - Retrocopy retro_mmul

						
>retro_mmul_2292
GCCGCCGCCGCCGCCGCTCTGGCAGACCTCGAATACTGCCCAGAGGTGAAACTAAAAACAACAGGATTAGAGGCAGCGGC

CGAGGCAGAAACCGCAAAGGGAAATGGTGAAGCTGAGGACCAGGAAGAGAAAGAAGACCCTGAGAAAGAAAACATTGAAA

AAGAAGATGATGTAGATCAGCAACTTGCGAACATAGACCCGAGGTGGATAGAATCACCTAAAACCAATGGCCATCTTGAA

AATGGCCCATTCTCACTGGAGCAGCAACTGGACGATGAAGAGGATAATGAAGAAGACTGCCCAAATCCTTAGGAATATAA

TCTTGATGAGCCAAATGCAGAAAGTGATTACACATACAGCAGCTCCTATGAACAATTCAACAGTGAATTGCCAAATGGAC

GGCATAAAATTCCCGAGTCACAGTTTCCAGAGTTTTCCACCCAGTTGTTCTCTGGATCCTTAGAACCTGTGGCCTGCGGC

TCTGTGCTTTCTGAGGGATCACCACTTACTGAGCAAAGGGAAAGCAGTCCGTCCCATGACAAAAGCAGGACGGTTTCAGC

CTGCAGTACTGGGGATTTGCCAAAAGCCAAAACCCAGGAGGCTGACTTGTTGGTGAACCCCCTGGATCCACGAAATGCTG

ATAAAATTAGAGTAGAAATTGTTGACCTGGGAAATGCTTGTTGGGTGCATAAACACTTCACGGAAAACATCCAGATGCGT

CAGCACCGTTCCGTAGAGGTTTTAATAGGAACGGGATACAGCACCCCTGCGGACATCTGGAGCATGGCATGTATGGCATT

TGAGCTGGCAACGGGCGATTATTTGTTTGAACCACATTCTGGGGAAGACTGTTCCAGAGACGAAGATCACATAGCATTGA

TCATTGAACTGCGGGGGAAAGTCCCTCGAAAATACGCTATGTTGGGGAAATGTTTCAAGGAGTTTTTCACCAGAAAAGGA

GAACTGCGACATGACCATGCCGAAGCCCTGATGCCCTTTTGATGTACTTGTGGAGAAGTATGGCTGGCCCCATGAAGATA

CTGCACAGTTTACAGATTTCCTGATCCCGATGTTAGAGATGGTTCCCGAAAAAACGAGCCTCAGCTGGCTAATGCCTTCG

GCATCCTTGGTTGAATTCT

ORF - retro_mmul_2292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.07 %
Parental protein coverage:	55.46 %
Number of stop codons detected:	3
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalSAAPSNDQDGEYCPEVKLKTTGLEEAAETETAKDNGEAEDQEEKEDAEKENIEKDEDDVDQELANIDPTW
		.AA.....D.EYCPEVKLKTTGLE.AAE.ETAK.NGEAEDQEEKED.EKENIEK.EDDVDQ.LANIDP.W
RetrocopyAAAAAALADLEYCPEVKLKTTGLEAAAEAETAKGNGEAEDQEEKEDPEKENIEK-EDDVDQQLANIDPRW
ParentalIESPKTNGHIENGPFSLEQQLDDEEDDEEDCPNPEEYNLDEPNAESDYTYSSSYEQFNGELPNGRHKIPE
		IESPKTNGH.ENGPFSLEQQLDDEED.EEDCPNP.EYNLDEPNAESDYTYSSSYEQFN.ELPNGRHKIPE
RetrocopyIESPKTNGHLENGPFSLEQQLDDEEDNEEDCPNP*EYNLDEPNAESDYTYSSSYEQFNSELPNGRHKIPE
ParentalSQFPEFSTSLFSGSLEPVACGSVLSEGSPLTEQEESSPSHDRSRTVSASSTGDLPKAKTRAADLLVNPLD
		SQFPEFST.LFSGSLEPVACGSVLSEGSPLTEQ.ESSPSHD.SRTVSA.STGDLPKAKT..ADLLVNPLD
RetrocopySQFPEFSTQLFSGSLEPVACGSVLSEGSPLTEQRESSPSHDKSRTVSACSTGDLPKAKTQEADLLVNPLD
ParentalPRNADKIRVKIADLGNACWVHKHFTEDIQTRQYRSIEVLIGAGYSTPADIWSTACMAFELATGDYLFEPH
		PRNADKIRV.I.DLGNACWVHKHFTE.IQ.RQ.RS.EVLIG.GYSTPADIWS.ACMAFELATGDYLFEPH
RetrocopyPRNADKIRVEIVDLGNACWVHKHFTENIQMRQHRSVEVLIGTGYSTPADIWSMACMAFELATGDYLFEPH
ParentalSGEDYSRDEDHIAHIIELLGSIPRHFALSGK-YSREFFNRRGELRHITKLKPWSLFDVLVEKYGWPHEDA
		SGED.SRDEDHIA.IIEL.G..PR..A..GK..SR.F.....E....T..KP...FDVLVEKYGWPHED.
RetrocopySGEDCSRDEDHIALIIELRGKVPRKYAMLGK>VSRSFSPEK-ENCDMTMPKP*CPFDVLVEKYGWPHEDT
ParentalAQFTDFLIPMLEMVPEK-RASAGECLRHPWLNS
		AQFTDFLIPMLEMVPEK.RASAG.CLRHPWLNS
RetrocopyAQFTDFLIPMLEMVPEK>RASAG*CLRHPWLNS

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0 .00 RPM	172 .33 RPM
SRP007412_brain_prefrontal_cortex	0 .00 RPM	148 .35 RPM
SRP007412_cerebellum	0 .00 RPM	117 .72 RPM
SRP007412_heart	0 .00 RPM	18 .31 RPM
SRP007412_kidney	0 .00 RPM	19 .25 RPM
SRP007412_liver	0 .00 RPM	4 .79 RPM
SRP007412_testis	20 .77 RPM	527 .52 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2292 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2292 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_2292 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000641	2 retrocopies	retro_chof_1584, retro_chof_904,
Macaca mulatta	ENSMMUG00000022732	1 retrocopy	retro_mmul_2292 ,

	RetrogeneDB ID:	retro_mmul_2292
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	8:65417015..65418154(+)
	Located in intron of:	ENSMMUG00000009144
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SRPK2
	Ensembl ID:	ENSMMUG00000022732
	Aliases:	SRPK2, SRPK3, STK23
	Description:	SRSF protein kinase 2 [Source:RefSeq peptide;Acc:NP_001244401]

Parental	SAAPSNDQDGEYCPEVKLKTTGLEEAAETETAKDNGEAEDQEEKEDAEKENIEKDEDDVDQELANIDPTW
	.AA.....D.EYCPEVKLKTTGLE.AAE.ETAK.NGEAEDQEEKED.EKENIEK.EDDVDQ.LANIDP.W
Retrocopy	AAAAAALADLEYCPEVKLKTTGLEAAAEAETAKGNGEAEDQEEKEDPEKENIEK-EDDVDQQLANIDPRW

Parental	IESPKTNGHIENGPFSLEQQLDDEEDDEEDCPNPEEYNLDEPNAESDYTYSSSYEQFNGELPNGRHKIPE
	IESPKTNGH.ENGPFSLEQQLDDEED.EEDCPNP.EYNLDEPNAESDYTYSSSYEQFN.ELPNGRHKIPE
Retrocopy	IESPKTNGHLENGPFSLEQQLDDEEDNEEDCPNP*EYNLDEPNAESDYTYSSSYEQFNSELPNGRHKIPE

Parental	SQFPEFSTSLFSGSLEPVACGSVLSEGSPLTEQEESSPSHDRSRTVSASSTGDLPKAKTRAADLLVNPLD
	SQFPEFST.LFSGSLEPVACGSVLSEGSPLTEQ.ESSPSHD.SRTVSA.STGDLPKAKT..ADLLVNPLD
Retrocopy	SQFPEFSTQLFSGSLEPVACGSVLSEGSPLTEQRESSPSHDKSRTVSACSTGDLPKAKTQEADLLVNPLD

Parental	PRNADKIRVKIADLGNACWVHKHFTEDIQTRQYRSIEVLIGAGYSTPADIWSTACMAFELATGDYLFEPH
	PRNADKIRV.I.DLGNACWVHKHFTE.IQ.RQ.RS.EVLIG.GYSTPADIWS.ACMAFELATGDYLFEPH
Retrocopy	PRNADKIRVEIVDLGNACWVHKHFTENIQMRQHRSVEVLIGTGYSTPADIWSMACMAFELATGDYLFEPH

Parental	SGEDYSRDEDHIAHIIELLGSIPRHFALSGK-YSREFFNRRGELRHITKLKPWSLFDVLVEKYGWPHEDA
	SGED.SRDEDHIA.IIEL.G..PR..A..GK..SR.F.....E....T..KP...FDVLVEKYGWPHED.
Retrocopy	SGEDCSRDEDHIALIIELRGKVPRKYAMLGK>VSRSFSPEK-ENCDMTMPKP*CPFDVLVEKYGWPHEDT

Parental	AQFTDFLIPMLEMVPEK-RASAGECLRHPWLNS
	AQFTDFLIPMLEMVPEK.RASAG.CLRHPWLNS
Retrocopy	AQFTDFLIPMLEMVPEK>RASAG*CLRHPWLNS

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_mmul_2292