RetrogeneDB ID:

retro_ogar_140

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873570.1:12747127..12749386(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000031494
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSOGAG00000009837
Aliases:None
Description:SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]


Retrocopy-Parental alignment summary:






>retro_ogar_140
ATGGAAGACGATAAGCGGTACCGTGTAAGAGTCTATGTCTTGAAAGAAAACCAGCAATGGGATGAGATCGGTGCCGGGCA
AATCTCCGCCACCTATGTTGAGGAACTCCGGGACGTATTTCTCCTCGTACGTTCGGAGTCAGACAGTTCACTGATCTTGG
AGTCGAGAATACAGCCAAACACCATCTATCAGAAGCAACAGGGGACGGTGATCGTTTGGTCTGAAGAAGAGAATCACGGT
TTGGCGTTAAGCTTTGAAGACGCCGACGGCTGTCGAGAAATCTGGGAAGACATCTGCCACATTCAAGGTAAAGATCCCAC
CATTGAAATTACACAAGCTCTTTTGAGTGAGTTACGAGAGCAAATTAGCGAAATGCCTGACATCTTTAATATAGTTGAGC
TCCCAGACTGTGAACTCGATACACTCGGGCAAATTGCCGACTTAATTAACTCAATTCTCGCCTCCGCTGACGGCAGGGAA
AAGATGGCTGTGATACTGGAAAGTGACGATTATATTAAAAAGTTACTGCAGCTTTTCCGCGCTTGTGAAATCCTGCAAAA
TATGAAATCCTTACACTATTTGCATGAAATTATTAAGGGGATTTTATGCCTTAATAAGACACCTCTGACTGAGGTTATGT
TTTCTGACGAGTGTATCTTGGATGTGGTGGGATGTCTTGAATATGACCCTGCTTTTCCTGAGCCAAAACGCTATCGAGAA
TTTTTGACCCAAAATGCCAAGTTCAAGGAGGTTATACCAATAGCAGACATTGAACTGAGGCAAAAAATACATCAGACTTA
CAGGGCGCAGTTCATTTATGACATTCTTTTGCCTGTCCCAACCGTGTTCGACGAGAATTATCTTTCTACGATTACGACGT
TTATTTTTTTCAATAAGGTTGAGATAGTTAGCATGCTGCAGGGTGATGACAAGTTTTTGACTGAAGTTTTCGCACAGTTA
AAGGATAAAACTACAAGTGATGATAAACGGTACGAATTGCTGTCTTTTTTCAAAGAATTCTGTAACTTTTCTCGCACATT
ACAGCCTCAAAGCAAAGATGCATTGTTCAAAACGTTGACACATTTGGGAATTCTTCCGGTTCTTAAAATCATTATGAGCG
CGGAAAATTTGCCAATTAGGTCAACTGCTACCGATATATTTGCTTATATAATAGAGTACAACCCGTCTTTAATCCGAAAA
TTCGCAATAGAAGAAGCCCGTAAGGGCGGGGATCATGACTTTCTCATTAACATAGTAATTTCACAGATGATCTGTGATAC
TGATCCTGAGCTGGCAGGTGCTATTCATTTGATGGAAATTATTCGTGCTCTCCTTGATCCAGAGACCATGGTGACGACAT
CGAGTAAATGTGAAAGAAGTGAGTTTTTAAATTTCTTCTATAAACGTTGCATGAATAAGTTGGTGGCACCACTTATGGCC
ACCACTTCAGAAGAGATAAGTGAGGAAGAGAATATAGATGGCTCTAATGAAAACATAACTTCTCTCAATTATCAAAGAGC
ACATCTGCTTTCTTTAATTGTAGAGCTACTTTCATTTTGTGTACAACATCACACATATTACATAAAAAATTATATTTTCA
ACAAAGACTTGCTAAGAAAAGTCTTGATCTTGATGAAGTCAAAGCATACTTTTGTGATCTTGTGTGCTATTCGCTTTATG
AGAAATATAGTTGGACTTAAAGATGAATTTTATAATCGTTACATCATCAAAGGAAATTTTTTAGAGCCAGTTGTAACTGC
TTTTCTGGACAATGGGACTCGATACAATATGTTAAATTCAGCTATTATTGAGATGTTTGACTACATAAGAGTCGAAAATA
TCAAGTCTCTTGTTGCACACATAATGGAAAATTATTATAAGAGTCTTGAAGAGATTGAGTATGTTCAGACATTCAAAGGA
TTGAAGGTTAGATATGAGCAAGAGAAAGAAAGACAAAAGAAAATACGAAAAAATTTACATTGTGTTCTCGGTAGCAAATT
ATATCGCAAAAGAGCCAAAATCTTGGAGGTGAAGGAAGAAACCTATTCCAAGGCAGAAGAAGAAGATGATGATGTGATGC
CTCCACTGGAAGACGAAATTCCAGATTATTATGAACAGTGTACTCACACTAAAGAAAGAGAAAAAGAAGATAAGGTAGAC
ACTCCCCAAAGAACATCTTCTGGTAGCTTCGAAGTTTCTTCGACTTGCTCTGCTGATCCTGAGAATACAGCAAGTAGCCC
AAGTGATCAAAGAGTAGTT

ORF - retro_ogar_140 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.24 %
Parental protein coverage: 57.36 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLIVW
D.R.RV.VY.L.E..QWD..G.G..S.TYVEEL....LLVR.ESD.SL.LES.I.PNT.YQKQQ.T.IVW
RetrocopyDKRYRVRVYVLKENQQWDEIGAGQISATYVEELRDVFLLVRSESDSSLILESRIQPNTIYQKQQGTVIVW
ParentalSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELNKL
SE.EN..LALSF....GC.EIWE.IC..QGKDP..E.TQ.L..E..E....EMP.......LP.CEL..L
RetrocopySEEENHGLALSFEDADGCREIWEDICHIQGKDPTIEITQALLSELREQ-ISEMPDIFNIVELPDCELDTL
ParentalEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLFEV
..IADL..S.L.S...REK.A..LE...YIKKLLQLF.ACE.L.N...LH.L.EII.GIL.LNK..L.EV
RetrocopyGQIADLINSILASADGREKMAVILESDDYIKKLLQLFRACEILQNMKSLHYLHEIIKGILCLNKTPLTEV
ParentalMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTPSV
MFSDECI.DVVGCLEYDPA...PKR.REFLT..AKFKEVIPI.D.ELRQKIHQTYR.Q.I.DI.LP.P.V
RetrocopyMFSDECILDVVGCLEYDPAFPEPKRYREFLTQNAKFKEVIPIADIELRQKIHQTYRAQFIYDILLPVPTV
ParentalFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQNR
F.EN.LST.T.FIFFNKVEIVSMLQ.D.KFL.EVFAQL.D..T.DDKR.EL..FFKEFC.FS.TLQPQ..
RetrocopyFDENYLSTITTFIFFNKVEIVSMLQGDDKFLTEVFAQLKDKTTSDDKRYELLSFFKEFCNFSRTLQPQSK
ParentalDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVIEQ
DA.FKTL..LGILP.L.I.M....L..RS.ATDIF.Y..E..PS..R.F...EA....D...LIN.VI.Q
RetrocopyDALFKTLTHLGILPVLKIIMSAENLPIRSTATDIFAYIIEYNPSLIRKFAIEEARKGGDHDFLINIVISQ
ParentalMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEK
MICDTDPEL.GA..LM...R.L.DPE.M..T..K.E.SEFLNFFY..CM..L.APL...TSE...E.
RetrocopyMICDTDPELAGAIHLMEIIRALLDPETMVTTSSKCERSEFLNFFYKRCMNKLVAPLMATTSEEISEE

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_140 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSOGAG00000009837 1 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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