RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_7
ATGGCAAACAACAGCGGCTCCAAAGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC

CTTTGGAGACGTTTATCTGGGCATCACCACCACCAACGGCGAGGAAGTAGCAGTGAAGCTGGAATCTCAGAAAGTCAAGC

ACCCCCAGTTGCTGTATGAGAGCAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT

CAGGAAAAAGACAACAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG

GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTAC

ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG

GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA

TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT

TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAGGGCTATGACAAAAAAACAAAAATATGAAAAGATTAGTGAGAAGAAG

GTGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG

CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT

ACACATTTGATTGGACGATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA

ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAAGATAACTAA

ORF - retro_ptro_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.81 %
Parental protein coverage:	71.63 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalELRVGNKYRLGRKIGSGSFGDIYLGANIASGEEVAIKLECVKTKHPQLHIESKFYKMMQGGVGIPSIKWC
EL.VG.KY.L.RKIGSGSFGD.YLG.....GEEVA.KLE..K.KHPQL..ESK.Y...QGGVGIP...W.
RetrocopyELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEEVAVKLESQKVKHPQLLYESKLYTILQGGVGIPHMHWY
ParentalGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKK
G.E.D.NV.VM.LLGPSLEDLFNFCSR.F..KTVL.LADQMISRIEY.H.KNF.HRD.KPDNFLMG.G..
RetrocopyGQEKDNNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPDNFLMGTGRH
ParentalGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSL
.N....IDFGLAKKYRD.RT.QHIPYRE.K.L.GT.RYASIN.HLGIEQSRRDD.ESLGYV.MYFN..SL
RetrocopyCNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYVFMYFNRTSL
ParentalPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFSTYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQG
PWQGL.A.TK.QKYE.ISEKK.STP.EVLCKG.P.EF..YLN.CR.LRF...PDY.YLRQLFR.LF....
RetrocopyPWQGLRAMTKKQKYEKISEKKVSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQLFRILFRTLN
ParentalFSYDYVFDWNMLKFGAAR
..YDY.FDW.MLK..AA.
RetrocopyHQYDYTFDWTMLKQKAAQ

                            

                            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_prefrontal_cortex	0 .07 RPM	121 .94 RPM
SRP007412_cerebellum	0 .14 RPM	131 .96 RPM
SRP007412_heart	0 .00 RPM	52 .14 RPM
SRP007412_kidney	0 .05 RPM	47 .47 RPM
SRP007412_liver	0 .00 RPM	26 .15 RPM
SRP007412_testis	9 .27 RPM	16 .86 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_7 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_7 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_7 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_32
Gorilla gorilla	retro_ggor_984
Pongo abelii	retro_pabe_170
Macaca mulatta	retro_mmul_295
Callithrix jacchus	retro_cjac_2680

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000011583	1 retrocopy	retro_mmur_10,
Nomascus leucogenys	ENSNLEG00000015080	1 retrocopy	retro_nleu_117,
Pongo abelii	ENSPPYG00000011818	1 retrocopy	retro_pabe_170,
Pan troglodytes	ENSPTRG00000014365	1 retrocopy	retro_ptro_7 ,

	RetrogeneDB ID:	retro_ptro_7
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	13:36732530..36733544(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPTRG00000005793
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	CSNK1E
	Ensembl ID:	ENSPTRG00000014365
	Aliases:	None
	Description:	None

Parental	ELRVGNKYRLGRKIGSGSFGDIYLGANIASGEEVAIKLECVKTKHPQLHIESKFYKMMQGGVGIPSIKWC
	EL.VG.KY.L.RKIGSGSFGD.YLG.....GEEVA.KLE..K.KHPQL..ESK.Y...QGGVGIP...W.
Retrocopy	ELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEEVAVKLESQKVKHPQLLYESKLYTILQGGVGIPHMHWY

Parental	GAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKK
	G.E.D.NV.VM.LLGPSLEDLFNFCSR.F..KTVL.LADQMISRIEY.H.KNF.HRD.KPDNFLMG.G..
Retrocopy	GQEKDNNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPDNFLMGTGRH

Parental	GNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSL
	.N....IDFGLAKKYRD.RT.QHIPYRE.K.L.GT.RYASIN.HLGIEQSRRDD.ESLGYV.MYFN..SL
Retrocopy	CNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYVFMYFNRTSL

Parental	PWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFSTYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQG
	PWQGL.A.TK.QKYE.ISEKK.STP.EVLCKG.P.EF..YLN.CR.LRF...PDY.YLRQLFR.LF....
Retrocopy	PWQGLRAMTKKQKYEKISEKKVSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQLFRILFRTLN

Parental	FSYDYVFDWNMLKFGAAR
	..YDY.FDW.MLK..AA.
Retrocopy	HQYDYTFDWTMLKQKAAQ

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

RetrogeneDB ID:

retro_ptro_7