RetrogeneDB - Retrocopy retro_cfam

						
>retro_cfam_2047
CCTGTTAGTGAAGAAGAATTTGGATGTAACAGAGAAGACAGTGTGACTTTGTAAAAGAGGGGCACTATTGGAAACAAAAG

AAAAATATTCCCAAATGCCCTTGGGAGGACTGTAAGATGAACATCATAGGTGGAAAGGATGATTTGCCAGTGCATTTCTG

TGACATATGTGATTTGCCTATTGAAATCTTTGGGCCAGTGATTCCATGAAAATATACCTTTTGCTATGGCTGCACTAATT

TCTATGACAACAATGAAGATAAAATGTGTCCAGGCTGTGGTATTCCTGTACTGCTCATTGGGGAGCATATACGAGGTTCC

ATCTTCATGTGTAGCACTGTCCAAAGATACAAGAAAATGTATTTGTCTGAAAAAGCCTTACAAGGTCATATCAACCACTA

CCATACGAAAGCCGAAAAACTTAACTGTGCTCCACCTGAAAAGATTCATCATTGTATGCCTTCACCAACAACTGAAATCC

ACAAAATGCTCCTAGACAAGGACCATATGAGCCATATGCCATCAGAACAGCACATCGTGATGTCACCACTTCCTGTGCAA

CATGTGCCACATGAACACAATAATCAGCCACGGGAGGATCTTTGTGCTCCTTCAGCAGTTGTCTCCACCTTACCTCCTTC

AGTCCATCAAGAAACCGTTAGTATTTCAATAAGAGAACACAGCAATTTGATAATCGTCCTTGTTCAGGATGACTCAGATT

CCTGTGCTAAAGAACCATCACCACCTGCTCCAGCACCTGCTTATCATCATCCCGAATATCAAAGTCAATCAGTGGAATGG

CACCCTCACCAGATTATGCCTCTAGAGTACATGTACCCCCGACCCCTGCATCCCCCATCTCCTCCACCACCACTAAGCCA

GCCAATGTCATACCTCTCGAGGATTCAGATACTTCTCTCTTGGTTTGTGGTCATGTGCCATCTCCACCATTGACTTCT

ORF - retro_cfam_2047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	52.57 %
Parental protein coverage:	65.78 %
Number of stop codons detected:	1
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalPGDEEGFDYNEEERYD-CKGGELF-GNQRR-FPGHL-FWDFQINILGEKDDTPVHFCDKCGLPIKIYGRM
		P..EE.F..N.E.....CK.G.L..GN.R..FP..L...D...NI.G.KDD.PVHFCD.C.LPI.I.G..
RetrocopyPVSEEEFGCNREDSVT>CKRGALL<GNKRKIFPNAL<WEDCKMNIIGGKDDLPVHFCDICDLPIEIFGPV
ParentalIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMR
		IP.K..FCY.C........DKMCPGC..PV..I....RGS.FMCS.VQ..K..YLS...LQ.HINH.H..
RetrocopyIP*KYTFCYGCTNFYDNNEDKMCPGCGIPVLLIGEHIRGSIFMCSTVQRYKKMYLSEKALQGHINHYHTK
ParentalAGKPVTRASLENVHPPIAPPPAEIPDRFLMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRA
		A.K....A..E..H.....P..EI....L...DK.HMSH.P..QHI.M.P.P.QHVPHEH.NQP.ED..A
RetrocopyAEK-LNCAPPEKIHHCMPSPTTEIHKMLL---DKDHMSHMPSEQHIVMSPLPVQHVPHEHNNQPREDLCA
ParentalPPAELSMAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQPVVSHPH
		P.A..S..PP...SV.QET..IS.R.HSNLI.V..QDDS.S.A.EP.PPAPAPA.HHPEYQ.Q.V..HPH
RetrocopyPSAVVSTLPP---SVHQETVSISIREHSNLIIVLVQDDSDSCAKEPSPPAPAPAYHHPEYQSQSVEWHPH
ParentalHIMPPQQHYAPP---PPPPPPISHPMPH-PPQAAGTPHLVYSQAPPPPMTS
		.IMP....Y..P...P.PPPP.S.PM...P.....T..LV....P.PP.TS
RetrocopyQIMPLEYMYPRPLHPPSPPPPLSQPMSY<PLEDSDTSLLVCGHVPSPPLTS

							

							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
SRP012049_cerebellum	0 .00 RPM	36 .79 RPM
SRP017611_brain	0 .00 RPM	36 .60 RPM
SRP017611_kidney	0 .00 RPM	18 .29 RPM
SRP017611_liver	0 .00 RPM	10 .30 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_2047 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2047 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_2047 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_49
Pan troglodytes	retro_ptro_67
Gorilla gorilla	retro_ggor_164
Pongo abelii	retro_pabe_112

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031990	1 retrocopy	retro_cfam_2047 ,
Loxodonta africana	ENSLAFG00000029522	1 retrocopy	retro_lafr_711,
Pteropus vampyrus	ENSPVAG00000000781	1 retrocopy	retro_pvam_1043,

	RetrogeneDB ID:	retro_cfam_2047
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	X:18058253..18059211(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CBLL1
	Ensembl ID:	ENSCAFG00000031990
	Aliases:	None
	Description:	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21225]

Parental	PGDEEGFDYNEEERYD-CKGGELF-GNQRR-FPGHL-FWDFQINILGEKDDTPVHFCDKCGLPIKIYGRM
	P..EE.F..N.E.....CK.G.L..GN.R..FP..L...D...NI.G.KDD.PVHFCD.C.LPI.I.G..
Retrocopy	PVSEEEFGCNREDSVT>CKRGALL<GNKRKIFPNAL<WEDCKMNIIGGKDDLPVHFCDICDLPIEIFGPV

Parental	IPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMR
	IP.K..FCY.C........DKMCPGC..PV..I....RGS.FMCS.VQ..K..YLS...LQ.HINH.H..
Retrocopy	IP*KYTFCYGCTNFYDNNEDKMCPGCGIPVLLIGEHIRGSIFMCSTVQRYKKMYLSEKALQGHINHYHTK

Parental	AGKPVTRASLENVHPPIAPPPAEIPDRFLMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRA
	A.K....A..E..H.....P..EI....L...DK.HMSH.P..QHI.M.P.P.QHVPHEH.NQP.ED..A
Retrocopy	AEK-LNCAPPEKIHHCMPSPTTEIHKMLL---DKDHMSHMPSEQHIVMSPLPVQHVPHEHNNQPREDLCA

Parental	PPAELSMAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQPVVSHPH
	P.A..S..PP...SV.QET..IS.R.HSNLI.V..QDDS.S.A.EP.PPAPAPA.HHPEYQ.Q.V..HPH
Retrocopy	PSAVVSTLPP---SVHQETVSISIREHSNLIIVLVQDDSDSCAKEPSPPAPAPAYHHPEYQSQSVEWHPH

Parental	HIMPPQQHYAPP---PPPPPPISHPMPH-PPQAAGTPHLVYSQAPPPPMTS
	.IMP....Y..P...P.PPPP.S.PM...P.....T..LV....P.PP.TS
Retrocopy	QIMPLEYMYPRPLHPPSPPPPLSQPMSY<PLEDSDTSLLVCGHVPSPPLTS

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

RetrogeneDB ID:

retro_cfam_2047