RetrogeneDB - Retrocopy retro_ecab

						
>retro_ecab_1048
GATCAGGCCCGCGCATCTTCTGTATGTAGGAGATGGAATGAAGTTTTTCATATCCCTGACCTTTGGAGAAAGTTTGAATT

TGAACTGAACCAATCAGCAACTTTGTCTTTTCAAGGCACTCCTCGTGATCTCATTCAGCAGATCTTTAAAAGGCATGTTG

CCTGTCTCCAGTATGTCAGCTTTAAGGTTGATAGCAGTACTGAATCAGTAGAGGCTGCCTGCGATATACTTTCTCAGCTG

GAAAATGGTTCTCCACACCTTGGGCTTGATTTCTAGGGCCAATCCAAGTTTTACGAACGTGTCAAAGTCTCATTTTGTGT

CAGCACTTACACTTGCTTTTGTCAACTCAAAATCATTATCATCAATCAAACTTGAAGACCCACCAGTGGATGACCCTTCA

CTGAAGGTTCTGGTGGCCAATAATAGTGATACTCTAACACTCCTAAAAATGAGCAGCTGTCCTTATGTTTCATCTGATGG

AATCCTTTGTGTAGCTGATCATTGTCAAGGCCTTAGAGAACTGGCATTGAATTATTACATTCCAAATGATGAACTTCTCC

TGGCCCTTTCAAGTGAGACTCATGTTAACCTTGAACATCTTCGAATTGATGTTGTGAGTGAAAATCCTGGACAAATTAAA

TTTCATTCCATTAAAAAACAAAGTTGAGATGCACTTATTAAACACTCCCCTGGAGTTAATGTTGTCATATACTTCTTTTT

AAACGAAGAGGAATTTGAGACATTCTTCACAGAAGAATCCCCTGTCACTCATCTTTATATCGGTCGGTCAGTAAGCAAAG

CGGTCCTAGGACGGATAGGTCCTAACTGCCCACGCCTAGTTGAGTTAGTGGTGTGTGCAAACGTTCTTCAGACTCTTGGT

AATGAGCTGATCTGTATTGCTCAACACTGTAAAAACTGAACAGCCTTGGGCCTCAGTGCATGTGAAGTTTGCTGCAGTGC

CGTGGTTGAGTTTGTAAGGCTGGGTGGGAGGAGGCTCGCGCAGCTCTCTGTGATGGAGGAGGTTCTGACCCCGATGGGGA

TTACGGCCTGGATAAAATTCACGCTGAAGCCTCCAAATACCTGGGAAGAACGTGGTTCCCGGATGTCATGCCTGGCTGG

ORF - retro_ecab_1048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	70.48 %
Parental protein coverage:	87.38 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalDRAHASQVCRSWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESA
		D.A.AS.VCR.WN.VFH.PDLWR.FEFELNQ.AT.....T...LI.QI.KRH...LQYVSFKVDSS.ES.
RetrocopyDQARASSVCRRWNEVFHIPDLWRKFEFELNQSATLSFQGTPRDLIQQIFKRHVACLQYVSFKVDSSTESV
ParentalEAACDILSQLVNCSLKTLGL-ISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLV
		EAACDILSQL.N.S...LGL.IS.A.PSF....KSHF.SALT..FVNSKSLSS.K..D.PVDDPSLKVLV
RetrocopyEAACDILSQLENGS-PHLGL>ISRANPSFTNVSKSHFVSALTLAFVNSKSLSSIKLEDPPVDDPSLKVLV
ParentalANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSEN
		ANNSDTL.LLKMSSCP.VS..GILCVAD.C.GLRELALNY....DELLLALSSE.HV.LEHLRIDVVSEN
RetrocopyANNSDTLTLLKMSSCPYVSSDGILCVADHCQGLRELALNYYIPNDELLLALSSETHVNLEHLRIDVVSEN
ParentalPGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPR
		PGQ..FH.I.K.S.DA.I.HSP.VN.V.YFFL.EEEF..FF..E.P.THLY.GRSVSK.VLGR.G..CPR
RetrocopyPGQIKFHSIKKQS*DALIKHSPGVNVVIYFFLNEEEFETFFTEESPVTHLYIGRSVSKAVLGRIGPNCPR
ParentalLVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLI-PDQK
		LVELVVCAN.L..L..ELI.IA..CKN..A.GL..CEV.CSA.VEFV...G.RL.QLS.MEEVL..PD..
RetrocopyLVELVVCANVLQTLGNELICIAQHCKN*TALGLSACEVCCSAVVEFVRLGGRRLAQLSVMEEVLT<PDGD
ParentalYSLEQIHWEVSKHLGRVWFPDMMPTW
		Y.L..IH.E.SK.LGR.WFPD.MP.W
RetrocopyYGLDKIHAEASKYLGRTWFPDVMPGW

							

							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
SRP021940_articular_cartilage	0 .00 RPM	29 .22 RPM
SRP021940_cerebellum	0 .00 RPM	21 .45 RPM
SRP021940_embryo	0 .00 RPM	13 .48 RPM
SRP021940_placental_villous	0 .00 RPM	16 .45 RPM
SRP021940_synovial_membrane	0 .00 RPM	14 .71 RPM
SRP021940_testis	0 .00 RPM	24 .87 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_1048 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_1048 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ecab_1048 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011128	3 retrocopies	retro_ecab_1048 , retro_ecab_1049, retro_ecab_1124,
Otolemur garnettii	ENSOGAG00000000250	1 retrocopy	retro_ogar_2765,

	RetrogeneDB ID:	retro_ecab_1048
Retrocopy location	Organism:	*Horse (Equus caballus)*
	Coordinates:	Un0872:7013..8132(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FBXL3
	Ensembl ID:	ENSECAG00000011128
	Aliases:	None
	Description:	F-box and leucine-rich repeat protein 3 [Source:HGNC Symbol;Acc:13599]

Parental	DRAHASQVCRSWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESA
	D.A.AS.VCR.WN.VFH.PDLWR.FEFELNQ.AT.....T...LI.QI.KRH...LQYVSFKVDSS.ES.
Retrocopy	DQARASSVCRRWNEVFHIPDLWRKFEFELNQSATLSFQGTPRDLIQQIFKRHVACLQYVSFKVDSSTESV

Parental	EAACDILSQLVNCSLKTLGL-ISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLV
	EAACDILSQL.N.S...LGL.IS.A.PSF....KSHF.SALT..FVNSKSLSS.K..D.PVDDPSLKVLV
Retrocopy	EAACDILSQLENGS-PHLGL>ISRANPSFTNVSKSHFVSALTLAFVNSKSLSSIKLEDPPVDDPSLKVLV

Parental	ANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSEN
	ANNSDTL.LLKMSSCP.VS..GILCVAD.C.GLRELALNY....DELLLALSSE.HV.LEHLRIDVVSEN
Retrocopy	ANNSDTLTLLKMSSCPYVSSDGILCVADHCQGLRELALNYYIPNDELLLALSSETHVNLEHLRIDVVSEN

Parental	PGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPR
	PGQ..FH.I.K.S.DA.I.HSP.VN.V.YFFL.EEEF..FF..E.P.THLY.GRSVSK.VLGR.G..CPR
Retrocopy	PGQIKFHSIKKQS*DALIKHSPGVNVVIYFFLNEEEFETFFTEESPVTHLYIGRSVSKAVLGRIGPNCPR

Parental	LVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLI-PDQK
	LVELVVCAN.L..L..ELI.IA..CKN..A.GL..CEV.CSA.VEFV...G.RL.QLS.MEEVL..PD..
Retrocopy	LVELVVCANVLQTLGNELICIAQHCKN*TALGLSACEVCCSAVVEFVRLGGRRLAQLSVMEEVLT<PDGD

Parental	YSLEQIHWEVSKHLGRVWFPDMMPTW
	Y.L..IH.E.SK.LGR.WFPD.MP.W
Retrocopy	YGLDKIHAEASKYLGRTWFPDVMPGW

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

RetrogeneDB ID:

retro_ecab_1048