RetrogeneDB - Retrocopy retro_mmus

						
>retro_mmus_2937
CAACCCCCTCCACAGCCACAGATTCCTAGCCCTGACAGGAAGGAACACAAAGGGACACCACAGTTCTGCTTAAGTCCAGC

TGCCCCGCAACATTCTGGAAAAAACATTCATTGGACGCCAGCCAGGGCACAGCCCTCGTGGAATCCTCATTAAAGAAGGT

GCACTCAAGTTAGTCGAGCTGAAACAGTTGGGCAAGATTACTGAATTTAGACCAACCTCAGCTCCTCTGTCCTCTCTCTC

AGCATTTGTTCTTCCTCAGGCTACAGCTGGGCCATCTTACCCTTGGGCAACAATCCCACCAGTATCCATCGCTGGGCAAC

CTAATGCAGTGGGTACATTCACTGAAATTCCTGATAGAAATATTCTAAAAGTTATCACTAAGAGGTTAACTGAATCAAAA

GTACTGTGCCTCATGCCTATGCTACTGCTGACCATGAACTTGGAGCAGTTTTAAAGGTTAGATGCGATCTGGTCAAAAAT

GACATTAAAGTCTCAGTAAATGACTTTATCATCAGAGCAGTAGCTGTTACTGTTAAACAAATGCCTGGGTTTAATGTCAC

CTGGAATGGAGAAGGACCAAACAGCTGCCTTCTGTTGACATTTCAATTGCTGTGGCTACAGATAAAGGTTTAATTACACC

AATCATAAAAGATGCAGCCGCTAAGGGCATATAGAAGATCGCTGACTCTGTTAAGGTTCTGTTGAAGAAAGCAAGAGATG

GAAAATTGATGCCGGAGGAGTACCAAGGAGGATCTTTTAGTATTTCCAACTTGTGGATATTTGGCATCAATGAGTTCACT

GCAGTGATTAACCTGCCTCAGTCCTGAATCTTGGAAGTTGGGAAATTCCACCCAGTGCTGAAGCTCACTGAGGATGAAGG

GGGAACCCCAACTGCAGCAGCACCAGCTTATCACTGTCACAGTGTCAAGTGACAGCAGGGTGGTTGATGATGAGCTAGCT

ATCAGGTTTCTTGAAACTTTCAAAGCAAACCTAGAGGGTCACATGTGACTTGGC

ORF - retro_mmus_2937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.48 %
Parental protein coverage:	68.06 %
Number of stop codons detected:	3
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalQPSPQPQIPCPARKEHKGTARFRLSPAA-RNILEKHSLDASQGTATGPRGIFTKEDALKLVELKQMGKIT
		QP.PQPQIP.P.RKEHKGT..F.LSPAA.RNILEK.......G....PRGI..KE.ALKLVELKQ.GKIT
RetrocopyQPPPQPQIPSPDRKEHKGTPQFCLSPAA>RNILEKTFIGRQPGHS--PRGILIKEGALKLVELKQLGKIT
ParentalESRPASAPPPSLSASVPPQATAGPSYPRPMTPPVSIPGQPNAAGTFTEIPASNIRRVIAKRLTESK-STV
		E.RP.SAP..SLSA.V.PQATAGPSYP....PPVSI.GQPNA.GTFTEIP..NI..VI.KRLTESK.STV
RetrocopyEFRPTSAPLSSLSAFVLPQATAGPSYPWATIPPVSIAGQPNAVGTFTEIPDRNILKVITKRLTESK<STV
ParentalPHAYATADCDLGAVLKVRRDLVKDDIKVSVNDFIIRAAAVTLKQMPGVNVTWDGEGP-KQLPSVDISVAV
		PHAYATAD..LGAVLKVR.DLVK.DIKVSVNDFIIRA.AVT.KQMPG.NVTW.GEGP.KQLPSVDIS.AV
RetrocopyPHAYATADHELGAVLKVRCDLVKNDIKVSVNDFIIRAVAVTVKQMPGFNVTWNGEGP<KQLPSVDISIAV
ParentalATDKGLITPIIKDAAAKGIQEIADSVKVLSKKARDGKLMPEEYQGGSFSISNLGMFGIDEFAAVINPPQA
		ATDKGLITPIIKDAAAKGI..IADSVKVL.KKARDGKLMPEEYQGGSFSISNL..FGI.EF.AVIN.PQ.
RetrocopyATDKGLITPIIKDAAAKGI*KIADSVKVLLKKARDGKLMPEEYQGGSFSISNLWIFGINEFTAVINLPQS
ParentalCILAVGRFRPVLKLTEDE-EGNP-QLQQHQLITVTMSSDSRVVDDELATRFLETFKANLENPMRLG
		.IL.VG.F.PVLKLTEDE..GNP.QLQQHQLITVT.SSDSRVVDDELA.RFLETFKANLE..M.LG
Retrocopy*ILEVGKFHPVLKLTEDE<RGNP<QLQQHQLITVTVSSDSRVVDDELAIRFLETFKANLEGHM*LG

							

							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	30 .89 RPM
SRP007412_cerebellum	0 .00 RPM	32 .96 RPM
SRP007412_heart	0 .00 RPM	102 .23 RPM
SRP007412_kidney	0 .00 RPM	46 .97 RPM
SRP007412_liver	0 .00 RPM	21 .55 RPM
SRP007412_testis	0 .00 RPM	50 .95 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2937 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2937 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2937 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2937 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_2937 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003998	1 retrocopy	retro_chof_2128,
Callithrix jacchus	ENSCJAG00000010888	1 retrocopy	retro_cjac_1425,
Mus musculus	ENSMUSG00000010914	1 retrocopy	retro_mmus_2937 ,

	RetrogeneDB ID:	retro_mmus_2937
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	7:60132670..60133684(+)
	Located in intron of:	ENSMUSG00000000948
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Pdhx
	Ensembl ID:	ENSMUSG00000010914
	Aliases:	Pdhx, AI481367, E3bp, Pdx1
	Description:	pyruvate dehydrogenase complex, component X [Source:MGI Symbol;Acc:MGI:1351627]

Parental	QPSPQPQIPCPARKEHKGTARFRLSPAA-RNILEKHSLDASQGTATGPRGIFTKEDALKLVELKQMGKIT
	QP.PQPQIP.P.RKEHKGT..F.LSPAA.RNILEK.......G....PRGI..KE.ALKLVELKQ.GKIT
Retrocopy	QPPPQPQIPSPDRKEHKGTPQFCLSPAA>RNILEKTFIGRQPGHS--PRGILIKEGALKLVELKQLGKIT

Parental	ESRPASAPPPSLSASVPPQATAGPSYPRPMTPPVSIPGQPNAAGTFTEIPASNIRRVIAKRLTESK-STV
	E.RP.SAP..SLSA.V.PQATAGPSYP....PPVSI.GQPNA.GTFTEIP..NI..VI.KRLTESK.STV
Retrocopy	EFRPTSAPLSSLSAFVLPQATAGPSYPWATIPPVSIAGQPNAVGTFTEIPDRNILKVITKRLTESK<STV

Parental	PHAYATADCDLGAVLKVRRDLVKDDIKVSVNDFIIRAAAVTLKQMPGVNVTWDGEGP-KQLPSVDISVAV
	PHAYATAD..LGAVLKVR.DLVK.DIKVSVNDFIIRA.AVT.KQMPG.NVTW.GEGP.KQLPSVDIS.AV
Retrocopy	PHAYATADHELGAVLKVRCDLVKNDIKVSVNDFIIRAVAVTVKQMPGFNVTWNGEGP<KQLPSVDISIAV

Parental	ATDKGLITPIIKDAAAKGIQEIADSVKVLSKKARDGKLMPEEYQGGSFSISNLGMFGIDEFAAVINPPQA
	ATDKGLITPIIKDAAAKGI..IADSVKVL.KKARDGKLMPEEYQGGSFSISNL..FGI.EF.AVIN.PQ.
Retrocopy	ATDKGLITPIIKDAAAKGI*KIADSVKVLLKKARDGKLMPEEYQGGSFSISNLWIFGINEFTAVINLPQS

Parental	CILAVGRFRPVLKLTEDE-EGNP-QLQQHQLITVTMSSDSRVVDDELATRFLETFKANLENPMRLG
	.IL.VG.F.PVLKLTEDE..GNP.QLQQHQLITVT.SSDSRVVDDELA.RFLETFKANLE..M.LG
Retrocopy	ILEVGKFHPVLKLTEDE<RGNP<QLQQHQLITVTVSSDSRVVDDELAIRFLETFKANLEGHMLG

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

RetrogeneDB ID:

retro_mmus_2937