RetrogeneDB - Retrocopy retro_mmul

						
>retro_mmul_1501
CCCTTTGATCATAGGGTTGTCCTACACAACGGTGATCCCAGTGAGCCTGTTTCAGATTACATCAATGCAACTATAACCGT

GCCTAAATTTGAAATCAAGTGCAACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCTGCAAAACACGG

TGAACGACTTTTGGCGGATGGTGTTCCAAGAAGACTCCCAGGTGATTGTCATGACAAGGAAAGAAATGGAGAGAGGAAAG

AGTAAATATGTCAAATATTGGCCTGATGAGTATGCTCTCAAAGCATATGGCGTCATGCGTGGTAGGAACGTCAAAGAAAG

CACCACTCATGACTATAAGCTAAGAGAACTTGAACTTTCAAAGGTTGGACAAGGGACTATGGAGAGAATGGTCTGGCAAT

ACCACTCTTGGAGCTGGCTGGGCCACGGAGTGCCCAGCGACCCCAGGGGCATGCTGGACTTCCTGGAGGAGGTGCACCAT

AAGCAGGGGAGCATCATGGATGCAGGGCCGTTTGTGGTGCACTGCAGTGCTGGCATTGGCCGGACAGGGACCTTCATTGT

GACTGATATTTTTATTGACATCATCAGAGAGAAAGGTGTTGACTGCAACATTGATGTTCCCAAAACCATCCACGTGGTGT

AGTCTCAGAGGTCAGGAATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCAGTCCAGTATTATATTGAAACA

CTACAGCGCAGGATTGAGGAAGAGCAGAAAAGCAAGAGGAAAGGGCACGAATATACAAATATTAAGTATTCTCTAGTGGA

CCAGATGAGTGGAGATCACAGCCCCCTCCTGCCTTATACTTCAGTGCCACCCTGTGCAGAAATGAGAGAAGACAGTGCTA

GAGTCTATGAAAATGTGGGCCTGGTGCAACAGCAGAAACGTTTAAGA

ORF - retro_mmul_1501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.52 %
Parental protein coverage:	52.28 %
Number of stop codons detected:	1
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVI
		PFDH.RVVLH.GDP.EPVSDYINA.I..P.FE.KCNNSKPKKSYIATQGCLQNTVNDFWRMVFQE.S.VI
RetrocopyPFDH-RVVLHNGDPSEPVSDYINATITVPKFEIKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQEDSQVI
ParentalVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTW
		VMT.KE.ERGKSK.VKYWPDEYALK.YGVMR.RNVKES..HDY.LREL.LSKVGQG..ER.VWQYH...W
RetrocopyVMTRKEMERGKSKYVKYWPDEYALKAYGVMRGRNVKESTTHDYKLRELELSKVGQGTMERMVWQYHSWSW
ParentalPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKT
		..HGVPSDP.G.LDFLEEVHHKQ.SIMDAGP.VVHCSAGIGRTGTFIV.DI.IDIIREKGVDC.IDVPKT
RetrocopyLGHGVPSDPRGMLDFLEEVHHKQGSIMDAGPFVVHCSAGIGRTGTFIVTDIFIDIIREKGVDCNIDVPKT
ParentalIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPC
		I..V.SQRSGMVQTEAQYRFIYMAVQ.YIETLQRRIEEEQKSKRKGHEYTNIKYSL.DQ.SGD.SPL.P.
RetrocopyIHVV*SQRSGMVQTEAQYRFIYMAVQYYIETLQRRIEEEQKSKRKGHEYTNIKYSLVDQMSGDHSPLLPY
ParentalTPTPPCAEMREDSARVYENVGLMQQQKSFR
		T..PPCAEMREDSARVYENVGL.QQQK..R
RetrocopyTSVPPCAEMREDSARVYENVGLVQQQKRLR

							

							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 .22 RPM	106 .78 RPM
SRP007412_brain_prefrontal_cortex	0 .00 RPM	85 .36 RPM
SRP007412_cerebellum	0 .06 RPM	55 .47 RPM
SRP007412_heart	0 .06 RPM	48 .93 RPM
SRP007412_kidney	0 .12 RPM	34 .62 RPM
SRP007412_liver	0 .00 RPM	10 .25 RPM
SRP007412_testis	0 .04 RPM	8 .82 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_1501 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1501 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_1501 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501 , retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516,
Nomascus leucogenys	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Pongo abelii	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,

	RetrogeneDB ID:	retro_mmul_1501
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	2:27227934..27228861(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PTPN11
	Ensembl ID:	ENSMMUG00000013253
	Aliases:	PTPN11, SHP2
	Description:	tyrosine-protein phosphatase non-receptor type 11 [Source:RefSeq peptide;Acc:NP_001248038]

Parental	PFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVI
	PFDH.RVVLH.GDP.EPVSDYINA.I..P.FE.KCNNSKPKKSYIATQGCLQNTVNDFWRMVFQE.S.VI
Retrocopy	PFDH-RVVLHNGDPSEPVSDYINATITVPKFEIKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQEDSQVI

Parental	VMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTW
	VMT.KE.ERGKSK.VKYWPDEYALK.YGVMR.RNVKES..HDY.LREL.LSKVGQG..ER.VWQYH...W
Retrocopy	VMTRKEMERGKSKYVKYWPDEYALKAYGVMRGRNVKESTTHDYKLRELELSKVGQGTMERMVWQYHSWSW

Parental	PDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKT
	..HGVPSDP.G.LDFLEEVHHKQ.SIMDAGP.VVHCSAGIGRTGTFIV.DI.IDIIREKGVDC.IDVPKT
Retrocopy	LGHGVPSDPRGMLDFLEEVHHKQGSIMDAGPFVVHCSAGIGRTGTFIVTDIFIDIIREKGVDCNIDVPKT

Parental	IQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPC
	I..V.SQRSGMVQTEAQYRFIYMAVQ.YIETLQRRIEEEQKSKRKGHEYTNIKYSL.DQ.SGD.SPL.P.
Retrocopy	IHVV*SQRSGMVQTEAQYRFIYMAVQYYIETLQRRIEEEQKSKRKGHEYTNIKYSLVDQMSGDHSPLLPY

Parental	TPTPPCAEMREDSARVYENVGLMQQQKSFR
	T..PPCAEMREDSARVYENVGL.QQQK..R
Retrocopy	TSVPPCAEMREDSARVYENVGLVQQQKRLR

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

RetrogeneDB ID:

retro_mmul_1501