RetrogeneDB ID:

retro_ecab_23

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:21091686..21093912(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002185
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSECAG00000013819
Aliases:None
Description:SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]


Retrocopy-Parental alignment summary:






>retro_ecab_23
ATGGAAGACAAAGGGCACCTTGTAAAGGTCTATATGCTTAATGAAGACCAAGAGTGGGACAATATAGGCATCGGCTACGT
CTCATTCACTTATGTGGAGCAGTTCGAGGGCGTGGCCATGCTGGTTCGATCTGAGTCGGACGACTCCGTGATCTTGGAGA
CAAAGATAAATACAAACGAGCCCTATCAGAAACAGCAAGGGACTTTAATTGTCTGGACTCATTCTGACAACCGTGATGTG
GCGTTAAGTTTCCAGGACGAAGGAAGTTGCCACGAGATCTGGGAAGCCATTTGCCGGCTTCAAGGAAACCCGACCATCGA
AATCACACAGGACCTGTTGGAAGAAGCCGGAGAGGAACCACCCGACGAAATGCTAGATCCCGGGAGTCTCATCGACCTGC
CGAACTGTGAGCTCAATACGCTTGAACAGATTTCTGCCTTAGTTACCTCGGTTCTCACCTCGCCTAGACGTGAGGAAAGT
CTGGCTGTGCTCTTGGAAAATGAGGACTATATTAAAAAGCTACTGCAGCTGTTCCACATTTGTGAGAACCTGCGGGATAT
GGAAGGCTTGCACTATTTGCATAAAATTATTAAAGGAATCTTATTCCTCAACAAGACCTCTCTGCTTGAGGTCCTTTTTT
CGGAAGAGTGTATCATGGATGTGGTGGGATGCCTTGAATACGATCCTGCTTTGGCTCAGCCGCAAAGGCATCGGGAATTC
CTGACCCAACATGCAAAGTTCAAGGAAGTTGTACCAATAACTGACTCTGAACTTAGGCAAAAAATACATCAGACGTACAG
GGCACAGTACATTTACGACATCGTTTTGCCTGTGCCATCCCCGTTTGAAGAGAATGTTCTTTCCACTGTTATTGCTTTTA
TTTTCTTCAACAAGGTTGAGATAGTCAGCATGCTGCAGGAAGATGACAAATTTTTGTCTGACGTTTTTGCACAGCTAAGA
GATAAGACTATCAGTGATGACAGACGGCGCGAATTGGTATTCTTTTTCAAGGAATTCTGTGAATTTTCTCAGAGTTTACA
GCCTGAAAGCAAGGATGCACTATTCACGACACTGACAGAATTGGGAATTCTTCCTGCTCTTAAAATTGTAATGAGCGTGG
ATGATTTGCAAATAAGGTCAGCTGCTACTGATATATTCACTTATCTGTTGGAGCACAGTCCATCCATGATCCAAGAATTT
ATAATGGAGGAAGCCCAGCAGAGTGAAGATGGTAACCTTTTCATCAATTTAGTAATTGGACAAATGGTCTCTGATCCTGA
TCCTGAGCTAGGAGGTGCTGTTCGTTCAGTGGAACTTCTTCGTGCTCTGCTTAATCCAGACAACATGCTGGGGACACCTG
GTAAATGTGAAAGAAGTGAATTTCTAAATTTCTTCTATAAACACTGTATGCATAACTTCATAGCACCACTTTTGGCCGCC
ACTTCAGAAGAGATTTGTGAAGAAAAGAATATAGCTGGATCTGACAAAAGCAACAAATATTGCTTCAATAATTATCAAAC
AGCACAGCTGCTTTCCTTAATTTTAGAGCTGCTCACATTTTGTGTGCAACATCACACATATCACATTAAAAGCTATATTT
TCAGCAAGGACTTGCTAAGAAGAGTCTTGATCTTGATGAATTCAAAGCACACTTTCCTGGTCTTGTCTGCTGTTCGCTTT
ATGAGAAGCATGGTTGGCCTCCAAGATGAATTTTATAATGATTACATCATCAAGGGAAATTTATTTCAGCCGGTTGTAAA
TGTCTTTCTGGATAATGGAAATCGGTACAATATGTTGAATTCAGCAGTTATTGAACTGTTCGAATACATAAGAGAGGAAA
ATATCAAGCCTCTTGTTGCACATATAGTTGAAAAGTTTTACAAGGCATTTGAATCGATTGAATATGTTCAGACATTCAAA
GGATTGAAGATTAACTATGAAAAAGAGAAAGACCAGCAGAGTCAAATACAGAAGAATTTACTTTCCACGCTGTTTCATAA
AGTGTTTCACAGCAGTAGCAAAGTCCTGGAGGAGAAGGAAGAAATGTGTTTTAAAGAAAGTAAAGAGGAAGAAGAAGCAG
TTAGGCCACCGTTGGAAGATGATTTTGAAGATCCTTCTGATAAGTTTGTGGAGACGACAAACCCAAAAGAAAATGAAGAC
AAGGTAGATCTTCCGAAAAGAACGTCTTCTGGCAACTTCAAGTTTACTTCATCCCATTCTGCGAGT

ORF - retro_ecab_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.58 %
Parental protein coverage: 90.91 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQASDT
M.D....VKVY.LNED..WD..G.G.VS.TYVE...G...LVR.ESD.S..LE.KIN.N..YQKQQ...T
RetrocopyMEDKGHLVKVYMLNEDQEWDNIGIGYVSFTYVEQFEGVAMLVRSESDDSVILETKINTNEPYQKQQG--T
ParentalLIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCE
LIVW....N.D.ALSFQ....C.EIWE.IC..QG..P..E.TQDL..E..EE...EM.....LIDLP.CE
RetrocopyLIVWTHSDNRDVALSFQDEGSCHEIWEAICRLQG-NPTIEITQDLLEEAGEEPPDEMLDPGSLIDLPNCE
ParentalLNKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKAT
LN.LE.I..LVTSVL.SP.R.E.LA..LENE.YIKKLLQLF..CENL...EGLH.L..II.GILFLNK..
RetrocopyLNTLEQISALVTSVLTSPRREESLAVLLENEDYIKKLLQLFHICENLRDMEGLHYLHKIIKGILFLNKTS
ParentalLFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILP
L.EV.FS.ECIMDVVGCLEYDPALAQP.RHREFLT..AKFKEV.PITDSELRQKIHQTYR.QYI.DI.LP
RetrocopyLLEVLFSEECIMDVVGCLEYDPALAQPQRHREFLTQHAKFKEVVPITDSELRQKIHQTYRAQYIYDIVLP
ParentalTPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQ
.PS.FEEN.LST...FIFFNKVEIVSMLQED.KFLS.VFAQL.D....DD.RRELV.FFKEFC.FSQ.LQ
RetrocopyVPSPFEENVLSTVIAFIFFNKVEIVSMLQEDDKFLSDVFAQLRDKTISDDRRRELVFFFKEFCEFSQSLQ
ParentalPQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINV
P...DA.F.TL..LGILPAL.IVM..DDLQ.RSAATDIF.YL.E.SPSM..EF.M.EAQQS.D..L.IN.
RetrocopyPESKDALFTTLTELGILPALKIVMSVDDLQIRSAATDIFTYLLEHSPSMIQEFIMEEAQQSEDGNLFINL
ParentalVIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDRCE
VI.QM..D.DPELGGAV....LLR.L..P.NML.T..K.E.SEFLNFFY.HCMH...APLL..TSE..CE
RetrocopyVIGQMVSDPDPELGGAVRSVELLRALLNPDNMLGTPGKCERSEFLNFFYKHCMHNFIAPLLAATSEEICE
ParentalKDNIVGSNKNSTICPGKYGSVQILAVLLALLTFCVEHHTYTIK-YIMNKDLLRRVLDLMNSKHTFLALCA
..NI.GS.K....C...Y...Q.L...L.LLTFCV.HHTY.IK.YI..KDLLRRVL.LMNSKHTFL.L.A
RetrocopyEKNIAGSDKSNKYCFNNYQTAQLLSLILELLTFCVQHHTYHIKSYIFSKDLLRRVLILMNSKHTFLVLSA
ParentalLRFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVVELFEFIRVEDIKSLTAHIVENFY
.RFMR...GL.DEFYN.YI.KGNLF.PV.N..LDNG.RYN.LNSAV.ELFE.IR.E.IK.L.AHIVE.FY
RetrocopyVRFMRSMVGLQDEFYNDYIIKGNLFQPVVNVFLDNGNRYNMLNSAVIELFEYIREENIKPLVAHIVEKFY
ParentalKALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKALEEDEEMWFNEDEEEEGKAVVA
KA.ESIEYVQTFKGLK..YE.EKD.Q.Q......S.L....F....K.LEE.EEM.F.E..EEE..AV..
RetrocopyKAFESIEYVQTFKGLKINYEKEKDQQSQIQKNLLSTLFHKVFHSSSKVLEEKEEMCFKESKEEE-EAVRP
ParentalPVEKSKSEDDFPDSYEKFMETKKAKESEDKENLPKRTSSGSFKFTFSHSTS
P.E......D..D........K......D...LPKRTSSG.FKFT.SHS.S
RetrocopyPLE--DDFEDPSDKFVETTNPKENEDKVD---LPKRTSSGNFKFTSSHSAS

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 24 .91 RPM
SRP021940_cerebellum 0 .00 RPM 21 .24 RPM
SRP021940_embryo 0 .03 RPM 50 .12 RPM
SRP021940_placental_villous 0 .14 RPM 34 .59 RPM
SRP021940_synovial_membrane 0 .03 RPM 24 .43 RPM
SRP021940_testis 2 .43 RPM 29 .61 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_23 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_23 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_23 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4799
Pan troglodytes retro_ptro_3191
Macaca mulatta retro_mmul_238
Oryctolagus cuniculus retro_ocun_9
Bos taurus retro_btau_232
Sus scrofa retro_sscr_1187
Canis familiaris retro_cfam_226
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000038431 retrocopy
retro_amel_48,
Bos taurus ENSBTAG000000005451 retrocopy
retro_btau_232,
Canis familiaris ENSCAFG000000028601 retrocopy
retro_cfam_226,
Equus caballus ENSECAG00000013819 1 retrocopy
retro_ecab_23 ,
Echinops telfairi ENSETEG000000024201 retrocopy
retro_etel_1699,
Felis catus ENSFCAG000000264571 retrocopy
retro_fcat_13,
Homo sapiens ENSG000001380411 retrocopy
retro_hsap_4799,
Loxodonta africana ENSLAFG000000178251 retrocopy
retro_lafr_791,
Myotis lucifugus ENSMLUG000000038751 retrocopy
retro_mluc_994,
Macaca mulatta ENSMMUG000000070011 retrocopy
retro_mmul_238,
Mustela putorius furoENSMPUG000000024351 retrocopy
retro_mputfur_92,
Nomascus leucogenys ENSNLEG000000093381 retrocopy
retro_nleu_1112,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
retro_ocun_9,
Otolemur garnettii ENSOGAG000000098371 retrocopy
retro_ogar_140,
Pan troglodytes ENSPTRG000000119331 retrocopy
retro_ptro_3191,
Sus scrofa ENSSSCG000000083981 retrocopy
retro_sscr_1187,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,




Copyright © RetrogeneDB 2014-2017