RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_831
AAGCATCTGACATCTGCCTGTCCAAATGTATATAGTATATCACAGTTTCATCATGCAACCCCGGACAATAAAACACACAG

TGGTGAGAAGTACACTGATCTTTTCAAACTCAGTTGGAGAGACTTGAAAGGTCTAAATGAGGACATTAGAAAGGAACTGC

TCCTGTCAACATTAGAACTTAAGGAAATGTCTGAGTAGTACTTTGATGGAAGAGGGAAAGCCTTCCGACTGATTATTGTG

TCACTAATGGACCAAGCATTCGGTATTCATCATGACAACTCCCGACATGTACAAGCCAGCCAGCGCACCATAGCCTTAAT

TCCAGAAATGATTCACATTGCTAGTCTGGTTCATGATTATGTTACTGGCGATGCAAGTTCTTGAAGAGCAAAACACACAG

TTAATAAGATCTGGGGTGAAAAGAAGGCTGTTCTTGCTGGAGACCTAACTCTTTCTGCAGCATCTATAGCTCTGGCACAA

ACTGGAAATAAAACTGTTGTATCTATTTTAACCCAAGTTATTGAAGATTTGGTGCATGGTGAATTTCTTCAGCTTGGGTC

AAAAGAAAATGAGAATGAAAGATTTGCACACTACCTTGAAAAGACCTTTAAGAAGACTGCCAGCTTGATAGCCAACAGTT

GTAAAGCAGTCTCTGTTCTAGGATGCCCCGGCCCAGTGGTGCATAAGATCACCTATCAGTATGGAAAAGTAGGAACAACT

TTTTAGCTAATAGATGATGTATTGGACCTCACCTCATGTTCTGACCAGATGGGCAAACCAACATCAGCTGATCTGAAGCT

TGGGTTAGCCACTGGTCCTGTCCTGTTGCCTGTCAGCAGTTCCTAGAAATGAATGCTCTGATCATGAGACAGTTCAGTTT

GCCTGGAGATGTAGACAGAGCTCGACAGTATGTGTTACAGAGTGATGGTGTGCAACAAACAACCTACCTCACCCAGCAGT

ACTACCACGAAGTGATAAGAGAGATCAGTAAACTTCGACCATCCCCAGAAAGAGATACCCTCATTCAACTTTCAGAAATT

GTACTCACAAGAGATAAA

ORF - retro_cjac_831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.94 %
Parental protein coverage:	85.3 %
Number of stop codons detected:	3
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalKHLTSACPNIYSISRFHHTTPDSKTHSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSELKEMSEYYFDG
		KHLTSACPN.YSIS.FHH.TPD.KTHSGEKYTD.FKL.WRDLKGL.EDIRKELL.ST.ELKEMSE.YFDG
RetrocopyKHLTSACPNVYSISQFHHATPDNKTHSGEKYTDLFKLSWRDLKGLNEDIRKELLLSTLELKEMSE*YFDG
ParentalKEKAFRPIIVALMARACNIHHNNSQHVQASQRTIALIAEMIHTASLVHDDVIDDASSRRGKHTVDKIWGE
		..KAFR.IIV.LM..A..IHH.NS.HVQASQRTIALI.EMIH.ASLVHD.V..DASS.R.KHTV.KIWGE
RetrocopyRGKAFRLIIVSLMDQAFGIHHDNSRHVQASQRTIALIPEMIHIASLVHDYVTGDASS*RAKHTVNKIWGE
ParentalKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDSVRSEFLQLGSKENENERFAHYLEKPFKKTASLI
		KKAVLAGDL.LSAASIALA..GN.TV.SILTQVIED.V..EFLQLGSKENENERFAHYLEK.FKKTASLI
RetrocopyKKAVLAGDLTLSAASIALAQTGNKTVVSILTQVIEDLVHGEFLQLGSKENENERFAHYLEKTFKKTASLI
ParentalANSYKAVSVLGCPDPVVHEIAYQYGKNIGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGPVLF-AC
		ANS.KAVSVLGCP.PVVH.I.YQYGK..G..F.LIDDVLD.TSCSDQMGKPTSADLKLGLATGPVL..AC
RetrocopyANSCKAVSVLGCPGPVVHKITYQYGK-VGTTF*LIDDVLDLTSCSDQMGKPTSADLKLGLATGPVLL<AC
ParentalQQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAVREISKLRPSPERDALIQLSEIV
		QQF.EMNA.IMR.FSLPGDVDRARQYVLQSDGVQQTTYL.QQY.HE..REISKLRPSPERD.LIQLSEIV
RetrocopyQQFLEMNALIMRQFSLPGDVDRARQYVLQSDGVQQTTYLTQQYYHEVIREISKLRPSPERDTLIQLSEIV
ParentalLTRDK
		LTRDK
RetrocopyLTRDK

							

							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
SRP051959_colon	0 .82 RPM	6 .66 RPM
SRP051959_heart	0 .47 RPM	2 .82 RPM
SRP051959_kidney	0 .55 RPM	2 .93 RPM
SRP051959_liver	0 .35 RPM	1 .69 RPM
SRP051959_lung	0 .75 RPM	4 .16 RPM
SRP051959_lymph_node	0 .98 RPM	5 .16 RPM
SRP051959_skeletal_muscle	0 .55 RPM	2 .31 RPM
SRP051959_spleen	0 .86 RPM	5 .02 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_831 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_831 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_831 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004695	1 retrocopy	retro_cjac_831 ,
Macaca mulatta	ENSMMUG00000005076	1 retrocopy	retro_mmul_1157,
Nomascus leucogenys	ENSNLEG00000016836	1 retrocopy	retro_nleu_2480,
Pan troglodytes	ENSPTRG00000002374	1 retrocopy	retro_ptro_2869,

	RetrogeneDB ID:	retro_cjac_831
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	11:15959058..15960116(+)
	Located in intron of:	ENSCJAG00000013223
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PDSS1
	Ensembl ID:	ENSCJAG00000004695
	Aliases:	None
	Description:	prenyl (decaprenyl) diphosphate synthase, subunit 1 [Source:HGNC Symbol;Acc:17759]

Parental	KHLTSACPNIYSISRFHHTTPDSKTHSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSELKEMSEYYFDG
	KHLTSACPN.YSIS.FHH.TPD.KTHSGEKYTD.FKL.WRDLKGL.EDIRKELL.ST.ELKEMSE.YFDG
Retrocopy	KHLTSACPNVYSISQFHHATPDNKTHSGEKYTDLFKLSWRDLKGLNEDIRKELLLSTLELKEMSE*YFDG

Parental	KEKAFRPIIVALMARACNIHHNNSQHVQASQRTIALIAEMIHTASLVHDDVIDDASSRRGKHTVDKIWGE
	..KAFR.IIV.LM..A..IHH.NS.HVQASQRTIALI.EMIH.ASLVHD.V..DASS.R.KHTV.KIWGE
Retrocopy	RGKAFRLIIVSLMDQAFGIHHDNSRHVQASQRTIALIPEMIHIASLVHDYVTGDASS*RAKHTVNKIWGE

Parental	KKAVLAGDLILSAASIALARIGNTTVISILTQVIEDSVRSEFLQLGSKENENERFAHYLEKPFKKTASLI
	KKAVLAGDL.LSAASIALA..GN.TV.SILTQVIED.V..EFLQLGSKENENERFAHYLEK.FKKTASLI
Retrocopy	KKAVLAGDLTLSAASIALAQTGNKTVVSILTQVIEDLVHGEFLQLGSKENENERFAHYLEKTFKKTASLI

Parental	ANSYKAVSVLGCPDPVVHEIAYQYGKNIGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGPVLF-AC
	ANS.KAVSVLGCP.PVVH.I.YQYGK..G..F.LIDDVLD.TSCSDQMGKPTSADLKLGLATGPVL..AC
Retrocopy	ANSCKAVSVLGCPGPVVHKITYQYGK-VGTTF*LIDDVLDLTSCSDQMGKPTSADLKLGLATGPVLL<AC

Parental	QQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAVREISKLRPSPERDALIQLSEIV
	QQF.EMNA.IMR.FSLPGDVDRARQYVLQSDGVQQTTYL.QQY.HE..REISKLRPSPERD.LIQLSEIV
Retrocopy	QQFLEMNALIMRQFSLPGDVDRARQYVLQSDGVQQTTYLTQQYYHEVIREISKLRPSPERDTLIQLSEIV

Parental	LTRDK
	LTRDK
Retrocopy	LTRDK

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

RetrogeneDB ID:

retro_cjac_831