RetrogeneDB ID:

retro_ecab_1049

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:Un1813:3896..5012(+)
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]


Retrocopy-Parental alignment summary:






>retro_ecab_1049
GATCAGGCCCGCGCATTTTCTGTATGTAGGAGATGGAACGAAGTTTTTCATATCCCTGACCTTTGGAGAAAGTTTGAATT
TGAACTGAACCAATCAGCAACTTTGTCTTTTCAAGCCACTCCTCGTGATCTCATTCAGCAGATCTTTAAAAGGCATGTTG
CCTGTCTCCAGTATGTCAGCTTTAAGGTTGATAGCAGTACTGAATCAGCAGAGGCTGCCTGCGATATATTTTCTCAGCTG
GGAAATGGTTCTCCACACCTTGGGCTTGATTTCTAGGGCCAATCCAAGTTTTATGAACGTGTCAAAGTCTCATTTTGTGT
CAGCACTTACACTTGCTTGTGTCAACTCAAAATCATTATCATCAATCAAACTTGAAGACCCACCCATGGATGACCCTTCA
CTGAAGGTTCTGGTGGCCAATAATAGTGATACTCTAACACTCCTAAAAATGAGCAGCTGTCCTTATGTTTCATCTGATGG
AATCCTTTGTGTAGCTGATCATTGTCAAGGCCTTAGAGAACTGGCATTGAATTATTACATTCCAAGTGATGAACTTCTGG
CCCTTTCAAGTGAGACTCATGTTAACCTTGAACATCTTCGAATTGATGTTGTGAGTGAAAATCCTGGACAAAGTAAATTT
CATTCCATTAAAAAACAAAGTTGAGATGCACTTATTAAACACTCCCCTGGAGTTAATGTTGTCATATACTTCTTTTTAAA
CGAAGAGGAATTTGTGACATTCTTCACAGAAGAATCCCCTGTCACTCATCTTTATTTCGGTCGGTCAGTAAGCAAAGCGG
TCCTAAGACGGATAGGTCCTATCTGCCCACGCCTAGTTGAGTTAGTGGTGTGTGCAAACGGTCTTCAGACTCTTGACAAT
GAGCTGATCTGTATTGCTCAACACTGTAAAAACTGAACAGCCTTGGGCCTCAGTGCATGTGAAGTTTGCTGCAGTGCCGT
GGTTGAGTTTGTAAGGCTGGGTGGGAGGAGGCTCGCGCAGCTCTCTGTGATGGAGGAGGTTCTGACCCGGATGGGGATTA
CGGCCTGGATAAAATTCACGCTGAAGCCTCCAAATACCTGGGAAGAACGTGGTTCCCGGATGTCATGCCTGGCTGG

ORF - retro_ecab_1049 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.74 %
Parental protein coverage: 87.38 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDRAHASQVCRSWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESA
D.A.A..VCR.WN.VFH.PDLWR.FEFELNQ.AT....AT...LI.QI.KRH...LQYVSFKVDSS.ESA
RetrocopyDQARAFSVCRRWNEVFHIPDLWRKFEFELNQSATLSFQATPRDLIQQIFKRHVACLQYVSFKVDSSTESA
ParentalEAACDILSQLVNCSLKTLGL-ISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLV
EAACDI.SQL.N.S...LGL.IS.A.PSFM...KSHF.SALT...VNSKSLSS.K..D.P.DDPSLKVLV
RetrocopyEAACDIFSQLGNGS-PHLGL>ISRANPSFMNVSKSHFVSALTLACVNSKSLSSIKLEDPPMDDPSLKVLV
ParentalANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSEN
ANNSDTL.LLKMSSCP.VS..GILCVAD.C.GLRELALNY...SDE.LLALSSE.HV.LEHLRIDVVSEN
RetrocopyANNSDTLTLLKMSSCPYVSSDGILCVADHCQGLRELALNYYIPSDE-LLALSSETHVNLEHLRIDVVSEN
ParentalPGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPR
PGQ..FH.I.K.S.DA.I.HSP.VN.V.YFFL.EEEF..FF..E.P.THLYFGRSVSK.VL.R.G..CPR
RetrocopyPGQSKFHSIKKQS*DALIKHSPGVNVVIYFFLNEEEFVTFFTEESPVTHLYFGRSVSKAVLRRIGPICPR
ParentalLVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLI-PDQK
LVELVVCANGL..LD.ELI.IA..CKN..A.GL..CEV.CSA.VEFV...G.RL.QLS.MEEVL..PD..
RetrocopyLVELVVCANGLQTLDNELICIAQHCKN*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






(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
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1049 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1049 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1049 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 ENSOGAG000000002501 retrocopy



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