RetrogeneDB ID:

retro_sscr_1187

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:X:25019985..25021867(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000012191
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSSSCG00000008398
Aliases:None
Description:SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]


Retrocopy-Parental alignment summary:






>retro_sscr_1187
CAACAAGGGACATTAATTGTTTGGTCTGAAGCTCAGAACCACGGTATGGCCATAAGTTTCCAGGACGCAGCATGTTGTCA
TGAGATCTGGAAAACCATTTGCCAGGTTCAAGGTAAAGACCCATCCGTCGAAATCACACAAGATCTCCTGGATGAATCAG
AAGAAGAACAATTTGAGAACTCACCGGAAACCTTTGAACTGCATGACCTGCCAAACTGCGAACTCGGTCAACTCCAACAG
ATCGCTGAGCTAGTTACCTCGGCTTTCACCTCACCTACACGTAAAGAAAGGCTGGCACTGGTCTTGGAAAATGAGGACTA
TATTAAAAAACTACTTCAGTTGTTCCATATTTGTGAGAACCTAGAGGATACTGAAGGCTTATACCATTTGTATGAAATCA
TTAAAGGAATTTTACTCCTCAACAAGACAGCTCTGCTTGAGGTAATGTTTTCTGATGAGTGTATCATGGATGTGGTGGGG
TGTCTTGAATATGACCCTGCTTTGGCTCAGCCAAAAAGGCATCGAGAATTCTTAACCCAAAATGCAAAGTTCAAGGAGGT
TATACCAATAACAAACTGTGAACTCCGGCAAAAAATACATCAGACATACAGGGTACAGTACATTCACAACATCCTTGTGC
CTGTACCATCCATGTTTGAAGATAATTTTCTTTCTACTCTTACAACTTTTATTTTTTTTAACAAGGTTAAGATAGTCAGC
ATGCTGCAGGAAGATGACAAATTTTTTGGGTGAAGTTTTTGCACAATTAAGGGATAACACCACAGGTGATGATAAACGGC
GTGAATTGCTGTTTTTTTTCAAGGAATTCTGTGCATTTTCTCAGACATTACAGCCTCAAAGCAAGGATGCACTTTTCACA
ACACTGACACAATTGGGAATTCTTCCTACTCTTAAAATTGTGATGGGCACGAGTGATTTGCAAATAAAGTCGGCTGCTAC
TGATATATTTACTTATCTAGTAGAGTATAGTCCATCTATGATCCGAGAATATATAATGAAAGAGGCCCAGAAGGATGAAG
ATGACAACCTTTTCATTAATTTAGTAATTGAACAAATGATGAGTGATACTGATCCTGAGCTAGGAGGTGCTGTTCACTTA
ATGGAACTTCTTCGCTCTCTGCTTGATCCAGACAACATGATGGCAACATCTAATAAATGTGAAAGAAGTGAATTTCTAAG
TTTCTTCTATAAATATTGTATACATAACATCATAGCACCACTTTTGTCAACTACTTCAGAAGATATATGTGAAGAGGATA
ATATAGTTGGCTCTGACAAAAACAACAAAAATTGCCTCAATAATTACCAAACCGCACAGCTGCTTGCCTTAATTTTAGAG
CTGCTTACATTTTGTGTGCAACATCACACATATTACATCAAAAACTGTATTTTGAGCAAAGACTTGCTAAGAAGAGTCTT
GATCCTGATGAATTCAAAGCACACTTTCCTGATCTTGTGTGCTCTTCGCTTTATGAGAAGGATGATTGGCCTTAAAGATG
AACTTTACAATTGTTACATCATCAAGGGAAATCTATTTGAGCCCATTGTAAATGCTCTTCTGGATAATGGAACTCGGTAC
AACTTGTTGAATTCAGCTATTATTGAGCTGTTTGAATACATAAGAGTAGAAAATATCAAGTCTCTCATTGCACATATAGT
TGAAAAGTTTTATGAAACACTTGAGTCAATTGAATATGTTCAGACATTCAAAGGATTGAAGATTAAATATGAGCAAGAAA
AAGACCGGCAGAGTCAAATACGGAAGAATTTGCGTTCTATACTGTATTGTAAAATATTTTGTGAAAGTGCCAGTGTCTTG
GAAGAGAAGGAAGAAGTCAGTTTTAAAGAAAATATAGAAGAA

ORF - retro_sscr_1187 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.09 %
Parental protein coverage: 82.94 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalKQDTLIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHMIDL
.Q.TLIVWSEA.N...A.SFQ..A.C.EIW..ICQVQGKDPSVE.TQDL.DESEEE.FE..PET....DL
RetrocopyQQGTLIVWSEAQNHGMAISFQDAACCHEIWKTICQVQGKDPSVEITQDLLDESEEEQFENSPETFELHDL
ParentalPTCELNKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFL
P.CEL..L..IA.LVTS...SP.R.E.LAL.LENE.YIKKLLQLF..CENLE.TEGL.HLYEII.GIL.L
RetrocopyPNCELGQLQQIAELVTSAFTSPTRKERLALVLENEDYIKKLLQLFHICENLEDTEGLYHLYEIIKGILLL
ParentalNKATLFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQD
NK..L.EVMFSDECIMDVVGCLEYDPALAQPKRHREFLT..AKFKEVIPIT..ELRQKIHQTYRVQYI..
RetrocopyNKTALLEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTQNAKFKEVIPITNCELRQKIHQTYRVQYIHN
ParentalIILPTPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKF-LSEVFAQLTDEATDDDKRRELVNFFKEFCAF
I..P.PS.FE.NFLSTLT.....NKV.IVSMLQED.KF.L.EVFAQL.D..T.DDKRREL....KEFCAF
RetrocopyILVPVPSMFEDNFLSTLTXXXXXNKVKIVSMLQEDDKF>LGEVFAQLRDNTTGDDKRRELLXXXKEFCAF
ParentalSQTLQPQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDI
SQTLQPQ..DA.F.TL..LGILP.L.IVMG..DLQ..SAATDIF.YLVE.SPSM.RE..M.EAQ...DD.
RetrocopySQTLQPQSKDALFTTLTQLGILPTLKIVMGTSDLQIKSAATDIFTYLVEYSPSMIREYIMKEAQKDEDDN
ParentalLLINVVIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTS
L.IN.VIEQM..DTDPELGGAV.LM.LLR.L.DP.NM.AT.NK.E.SEFL.FFY..C.H...APLL..TS
RetrocopyLFINLVIEQMMSDTDPELGGAVHLMELLRSLLDPDNMMATSNKCERSEFLSFFYKYCIHNIIAPLLSTTS
ParentalEDRCEKDNVVGSNKNSTVCPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTF
ED.CE.DN.VGS.KN...C..NYQTAQLLALILELLTFCV.HHTY.IKN.I..KDLLRRVL.LMNSKHTF
RetrocopyEDICEEDNIVGSDKNNKNCLNNYQTAQLLALILELLTFCVQHHTYYIKNCILSKDLLRRVLILMNSKHTF
ParentalLALCALRFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHI
L.LCALRFMRR.IGLKDE.YN.YI.KGNLFEP..NALLDNGTRYNLLNSA.IELFE.IRVE.IKSL.AHI
RetrocopyLILCALRFMRRMIGLKDELYNCYIIKGNLFEPIVNALLDNGTRYNLLNSAIIELFEYIRVENIKSLIAHI
ParentalVENFYKALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKTLEEDEEMWFNEDEEE
VE.FY..LESIEYVQTFKGLK.KYEQEKDRQ.Q......SIL....F...A..LEE.EE..F.E..EE
RetrocopyVEKFYETLESIEYVQTFKGLKIKYEQEKDRQSQIRKNLRSILYCKIFCESASVLEEKEEVSFKENIEE

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
SRP014902_placenta 0 .00 RPM 17 .26 RPM
SRP014902_testis 0 .00 RPM 46 .54 RPM
SRP018288_heart 0 .00 RPM 116 .30 RPM
SRP018288_kidney 0 .00 RPM 151 .01 RPM
SRP018288_liver 0 .00 RPM 107 .94 RPM
SRP018288_lung 0 .00 RPM 175 .04 RPM
SRP018856_adipose 0 .00 RPM 51 .07 RPM
SRP035408_brain 0 .19 RPM 156 .45 RPM
SRP035408_liver 0 .00 RPM 88 .54 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_1187 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_1187 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1187 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
Canis familiaris retro_cfam_226
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 ENSCAFG000000028601 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 ENSSSCG00000008398 1 retrocopy
retro_sscr_1187 ,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,


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