RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_170
ATGGCAAACAACAGCGGCTCCAAGGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC

CTTTGGAGACGTTTATCTGGGCATCACCACCACCAACGGCGAGGAAGTAGCAGTGAAGCTGGAATCTCAGAAGGTCAAGC

ACCCCCAGTTGCTGTATGAGAGCAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT

CAGGAAAAAGACAACAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG

GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTTC

ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG

GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA

TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT

TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAGGGCTATGACAAAAAAACAAAAATATGAAAAGATTAGTGAGAAGAAG

ACGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG

CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT

ACACATTTGATTGGACGATGTTAAAGCATAAAGCAGCACAGCAGGCAACCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA

ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAAGATAACTAA

ORF - retro_pabe_170 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....
RetrocopyPWQGLRAMTKKQKYEKISEKKTSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQLFRILFRTLN
ParentalFSYDYVFDWNMLKFGAAR
		..YDY.FDW.MLK..AA.
RetrocopyHQYDYTFDWTMLKHKAAQ

							

							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 .39 RPM	60 .76 RPM
SRP007412_cerebellum	1 .58 RPM	34 .17 RPM
SRP007412_heart	0 .54 RPM	14 .84 RPM
SRP007412_kidney	0 .27 RPM	28 .67 RPM
SRP007412_liver	0 .52 RPM	14 .20 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_170 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_170 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_170 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_32
Pan troglodytes	retro_ptro_7
Gorilla gorilla	retro_ggor_984
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_pabe_170
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	13:36900432..36901446(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPPYG00000005290
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	CSNK1E
	Ensembl ID:	ENSPPYG00000011818
	Aliases:	None
	Description:	casein kinase 1, epsilon [Source:HGNC Symbol;Acc:2453]

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	PWQGLRAMTKKQKYEKISEKKTSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQLFRILFRTLN

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

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

RetrogeneDB ID:

retro_pabe_170