RetrogeneDB ID:

retro_cfam_226

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:22666641..22668993(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000013598
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSCAFG00000002860
Aliases:None
Description:SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]


Retrocopy-Parental alignment summary:






>retro_cfam_226
ATGGCAGATAAGCGGCACCATGTAACACTCTACTCACTGAACCAGGACCAAGAATGGGAAGAGCTAGGCACCGGACACAT
CTCTTCCACTTACGTGGAACGCCTCCAGGGCGTGTTTCTGCTAGTTCAGTCTGATTCCCATGGCTCACTAATCTTGGAGT
CGAAGATAAATTCTAATACGCCTTATCAGAAACAACAGGAAACGCTGATTGTTTGGTCTGAAGCAGAGAACCATGGTATG
GCGTTAAGTTTCCAGGACACTGAAGGTTGTCGCCAGATCTGGGAAGACATTTGCCGGGTTCAAGGTAAAGACCCATCCGT
CGAAATCACGCAAGACCTCTTGGAAGAATCTGAAGACGAACAACTGGATGACATACTGGAAACTAATACTGTGCTTGTCC
TGCCTAACTGTGAACTCAGTAAACTTGAAGAGATTTCTGACCTAATTACCTCTGTTCTCCTTTCACCGATACATAAGGAA
AGACTGGCTCTGATCTTAGAAAATGAGGCCTATATTAAAAATTTGCTGCAGCTGTTCCGCGCTTGTGAGGACCTAGGAGA
CATCGCAAACTTACACTATTTGTATGAAATTATTAAAGGCATCTTATTCCTTAACAAGACGGGTCTGTTTGAGATCCTGT
TTTCTGCTGACTGTATCATGGATGTGGTGGGATGCCTCGAGTATGACCCTGCTTTGGCTCAGCCAAAAAGGCATAGGGAA
TTCTTGACCCAAAATGCAAGGTTCAAGGAAATTGTACCAATAACAGACTGTGAACTTATGCAAAAAATACATCAAACATA
CAAGGTGCAGTACATTTATGATATCCTTTTGCCTATACCATCCGTGTTTGAAGAGAACTTACTCTCTGCTCTTACAGCTT
TTATTTTCCTCAACAAGGTCGAGATAGTCAGCATGCTGCAGGAAGATGACAACTTTTTGCCTGAAGTGTTTGCACAGTTA
AGGGATGAGACTATAGATGATGATAAACGGCGTGAATTGCTATTTTTCTTCAAGGAATTTTGTGATTTTTCTCAGACATT
ACATCCTCCAAGGAAGGATGAGCTATTCAAAACTTTGACAGAATTGGGAGTTCTTCCTGTTCTTAAAGTTGTGATGAGCA
TGGAAGATGTGCAAATAAGGTCAGCTGCTACTGACATATTTACTTACCTTGTGGAGTATAGTCCATCCATGATTCGAGAA
TTTATTGTGGAAGAAGCCCAGCAGAGTGAAGACGGTAACCTTTTCATTAATTTAGTAATTGAGCAAATGATCTGCGACAA
TGATCCTGAGCTAGGAGGTGCTGTTCATCTAATGGGACTTCTTCGTGTTCTACTTGATCCTGAAAACATGCTAACAACAT
CTAATAAATGTGAGAGAAGCGAATTTCTGAATTTCTTCTATAAGCACTGTATACATATCTTCATAGCACCACTTTTTGCC
GCCACTGCTGAACGTATACATGAAGAGGATAATACAGCTGGATCCGACCAAAACAACAGAAATTGCCTCAATAATTATCA
AACAGCACAGCTGCTTTCTTTAATTTTAGAGCTGCTCACATTCTGTGTGGAACATCACACATACTACATAAAGAACTATA
TTTTGAGCAAAGACTTGCTAAGAAGAGTCTTGATCCTGATGAATTCAAAGCACACTTTCCTGATCTTATGTGCTCTCCGC
TTTATGAGAAGGATGATTGACCTTAAAGATGAACTTTATAATTCTTACATCATCAAGGGAAATCTCTTTGAACCAGTTGT
CAGTGCTTTCCTGGATAACGGAACTCGGTACAATATGTTAAATTCTGCTGTTATTGAGCTGTTTGAATACATAAGAGTGG
AAAATATCAAATCTCTGGTTGCACATATAGTTGAAAATTTTTATGAAACACTTGAATCGATTGAATATGTTCAGACATTC
AAAGGATTGAAGATTAAATATGAAGAAGAGAAAGACCGGCAAAGTCAAATACGGAAGAATTTACATTCTGTAACGTATAG
TAAAATATTTCACAGAAGTGCCAGAGTTTTGGAGAAGAAGGAAGAAAGATGTCTTAAAGAAAATTCAGAGGAAAGAGAAG
CAGTTAGGCCACCACTGGAAAATGATTTTCAAGGTCATTATGATAAATTTGTGGAGACTAAAAAACCAAAAGAAAATGAA
GACAGAGTAGATCTTCATAAGACAGCAACTTCTGGTGGCTACAAAATCACCTCATCCCATTCTGCTGGTACGGCTAATGG
AACAAGTAGCCTGAATGGTCGCAGCATGGTTGGCTTAGTGAATCGTCCTGATGAAGAAAAAGATAAGGAAGAAGAGACAT
CTCCCAGGAAAAGACAACATCTTAACCTGTAA

ORF - retro_cfam_226 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.19 %
Parental protein coverage: 85.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
M.D.R..V..Y.LN.D..W...GTGH.SSTYVE.L.G..LLV...S.GSL.LESKIN.NT.YQKQQ.TLI
RetrocopyMADKRHHVTLYSLNQDQEWEELGTGHISSTYVERLQGVFLLVQSDSHGSLILESKINSNTPYQKQQETLI
ParentalVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEIPETSHLIDLPTCELN
VWSEAEN...ALSFQ...GC..IWE.IC.VQGKDPSVE.TQDL..ESE.E....I.ET.....LP.CEL.
RetrocopyVWSEAENHGMALSFQDTEGCRQIWEDICRVQGKDPSVEITQDLLEESEDEQLDDILETNTVLVLPNCELS
ParentalKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
KLEEI.DL.TSVL.SPI..E.LAL.LENE.YIK.LLQLF.ACE.L.....LH.LYEII.GILFLNK..LF
RetrocopyKLEEISDLITSVLLSPIHKERLALILENEAYIKNLLQLFRACEDLGDIANLHYLYEIIKGILFLNKTGLF
ParentalEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
E..FS..CIMDVVGCLEYDPALAQPKRHREFLT..A.FKE..PITD.EL.QKIHQTY.VQYI.DI.LP.P
RetrocopyEILFSADCIMDVVGCLEYDPALAQPKRHREFLTQNARFKEIVPITDCELMQKIHQTYKVQYIYDILLPIP
ParentalSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
SVFEEN.LS.LT.FIF.NKVEIVSMLQED..FL.EVFAQL.DE..DDDKRREL..FFKEFC.FSQTL.P.
RetrocopySVFEENLLSALTAFIFLNKVEIVSMLQEDDNFLPEVFAQLRDETIDDDKRRELLFFFKEFCDFSQTLHPP
ParentalNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
..D..FKTL..LG.LP.L..VM.M.D.Q.RSAATDIF.YLVE.SPSM.REF...EAQQS.D..L.IN.VI
RetrocopyRKDELFKTLTELGVLPVLKVVMSMEDVQIRSAATDIFTYLVEYSPSMIREFIVEEAQQSEDGNLFINLVI
ParentalEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEKD
EQMICD.DPELGGAV.LMGLLR.L.DPENML.T.NK.E.SEFLNFFY.HC.H...APL...T.E...E.D
RetrocopyEQMICDNDPELGGAVHLMGLLRVLLDPENMLTTSNKCERSEFLNFFYKHCIHIFIAPLFAATAERIHEED
ParentalNIVGSNKNSTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCALR
N..GS..N...C..NYQTAQLL.LILELLTFCVEHHTY.IKNYI..KDLLRRVL.LMNSKHTFL.LCALR
RetrocopyNTAGSDQNNRNCLNNYQTAQLLSLILELLTFCVEHHTYYIKNYILSKDLLRRVLILMNSKHTFLILCALR
ParentalFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFYKA
FMRR.I.LKDE.YN.YI.KGNLFEPV..A.LDNGTRYN.LNSAVIELFE.IRVE.IKSL.AHIVENFY..
RetrocopyFMRRMIDLKDELYNSYIIKGNLFEPVVSAFLDNGTRYNMLNSAVIELFEYIRVENIKSLVAHIVENFYET
ParentalLESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKALEEDEEMWFNEDEEEEGKAVVAPV
LESIEYVQTFKGLK.KYE.EKDRQ.Q......S...S..F.R.A..LE..EE....E..EE...AV..P.
RetrocopyLESIEYVQTFKGLKIKYEEEKDRQSQIRKNLHSVTYSKIFHRSARVLEKKEERCLKENSEER-EAVRPPL
ParentalE
E
RetrocopyE

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 84 .50 RPM
SRP017611_brain 0 .00 RPM 58 .91 RPM
SRP017611_kidney 0 .00 RPM 85 .06 RPM
SRP017611_liver 0 .00 RPM 40 .32 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_226 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_226 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_226 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
Equus caballus retro_ecab_23
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 ENSCAFG00000002860 1 retrocopy
retro_cfam_226 ,
Equus caballus ENSECAG000000138191 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,




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