RetrogeneDB ID:

retro_ocun_9

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:X:13407434..13409777(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000006805
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSOCUG00000006880
Aliases:None
Description:SMEK homolog 2, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:29267]


Retrocopy-Parental alignment summary:






>retro_ocun_9
ATGGCGGATAGGCGGCACCGTGTAAGAATTTATGTCTTAAGTGACGACCATTTATGGGACAACATAGGAACCGGGCAAAT
CTCAATCAGTTACGTAGAGCGGCTGCAGGGCATGGCTCTGCTTGTTCGATCAGAGACTGATGGCTCGCTGCTCTTAGAGT
CAAAGATAAATCCCCAAACCCTCTATAAGAAACAGCAAGGGGTTCTGATAATTTGGTACGAAGCTGAGAATCATGGTATG
GCGCTGAGCTTCCAGGACATCGCAGGCTGTCGTGAGATCTGGGAGGGCATTTGCCAAGTCCAAGGTAAAGACCCCACTGT
CAAAGATCCTTTAGACAAATCAGAACGGCCGGTTGAAAAGGCAGATACCAGTACTCTAATTAAACTGCCTGTCTGTGAAC
TCAATACGCTTGAACAGATTGCAAACTTAGTTACTTCGGTACTTGCCTCACCTATCCTTAGGGAAAGGCTAGCTCGGATC
TTGGAACATGATAATTATATTAAAAAACTACTGCAGCTGTTCCACACTTGTGAGGACCAGCAAAACACTCAAGGGTTACA
CCATCTCCATGACATTATTAAAGGAATCTTATCCCTCAACAAGACAACCCTCTTGGAGATTTTATTTTCTGATGAGTGTA
TCATGGATGTGGTTGGATGCCTTGAATACGACCCTGCTTTGGCCCAACCAAAAAAGCATAGGGAATTCTTAACCCAAAAT
GCAAAGTTCAAGGAAGTTGTACCAATAACAGACTCTGAACTTAGAAAAAAAATACATCAGACATACAGAGTACAGTACAT
TTATGACATTCTTTTACCTGCGCCTTCCATGTTTGAAGAGAATTTTCTGTCTTCTCTTACAACTTTCATTTTCTTCAACA
AAGTTGAGATAGTCAGCATGCTTCAGGAAGATGAGAAGTTTTTGTTTCAAGTTTTTGCACAGTTAAAGGATGAGACTACA
GATAATGATAAACGGCTTGAACTGATGCTTTTTTTCAAGGATTTTTTTGCATTTTCTCAGACTTTAGAGCCTCACAGTAA
GGATATGCTGTTCAAAACATTGACACAATTGGGAATTCTTCCTGCTCTTAAAATGGTGATGAACATGAGTGATTTGCAAA
TTAAAACAGCTGCTACAGATATATTTACTTATCTAATGGAGTATAGCCCGTCCATGATCCGAGCATTTATAATGCAAGAA
GCAGAAAAGAGGGAGGATGAAGACCTTTTTATTAATATGATAATTGAACAAATTGTTGGTGATACTGATCCTGAGCTAGG
AGGTGCTTTTCATTTGGTGGGACTTCTTCGTTGTCTCCTTGATCCAGACAACATGCTGATAACAATTAATACGTGTGAAA
GAAGTGAATTTCTCAATTTTTTTTATAAACACTGTATGCATAACTTGATAGCACCACTTTTGGCCACCACTTCAGGAAGC
AAATGTGGTGAAGGTAATATAGTTGGGTCTGACAAATACAAACATTCCTCTAATAATTATCAAACGGCACAGCTGCTTAA
TTTAATTTTGGAACTACTCATATTTTGTGTGCAACATCACACATATTATATAAAGCACTATATTTTGAGCAACGATTTGC
TAAGAAGAGTCTTGATGTTGACTGAATCAAAGCACACCTTTCTGCTGTTGTGTGCTATCCGTTTTATGAGAAGGATGATT
GGCCTTAAAGATGAACTGTATAATCGTTACATCATCCAGGGAAATCTTTTTGAGCCAGTGGTAAAGGCTCTTCTTGACAA
TGGAACTCGGTACAATATGTTGAATTCGGCTATTATTGAGTTGTTTGAGTACATAAGAGTGGAAAACATCAAGTCTCTTG
TTGTACATGTAGTTGAGAATTATAATGTACTTCAATCTATTGAGTATGTGAAGACATTCAAGGGACTAAAGATTAAATAT
GAACAAGAGAAACACAGACAGAATCAAATACGGGAGAATTTACATTCCATGCTATATAGTAAAATACTTTGCCAAGGGGT
CAGTGTCTTGGATATGAAGGAAGAAGTGGGTTTTAATGAAGATATGAAAGATGCAGTTTTACCACCACTGGAAAATGACT
TTCCAGATGATGATACATTTATGGAGACTGAAGTGAGTGAAAATGAAGACAAGGTGAACCTTCCCAAAAGAACATCTTCT
GGCGGCTTCAAATTTTCTTCCTGTCATTCTGCAAATCCTGATGTTGGACCAAGTAGCGAAGACAGAAGCAGTGTGGTTGA
TGTACTGGACAATCCTGACACTGAAGAAAATGAAAACAATGAAGAAAATGAAAACAATGAAGAAACAGCAACCCCCAGAA
AAAGACCACATTGTAGTTCATAA

ORF - retro_ocun_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.09 %
Parental protein coverage: 86.34 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
M.D.R.RV..Y.L..D..WD..GTG..S..YVE.L.GM.LLVR.E.DGSLLLESKINP.T.Y.KQQ..LI
RetrocopyMADRRHRVRIYVLSDDHLWDNIGTGQISISYVERLQGMALLVRSETDGSLLLESKINPQTLYKKQQGVLI
ParentalVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
.W.EAEN...ALSFQ..AGC.EIWE.ICQVQGKDP.V....D..D.SE..R..E...TS.LI.LP.CELN
RetrocopyIWYEAENHGMALSFQDIAGCREIWEGICQVQGKDPTVK---DPLDKSE--RPVEKADTSTLIKLPVCELN
ParentalKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
.LE.IA.LVTSVL.SPI.RE.LA..LE...YIKKLLQLF..CE...NT.GLHHL..II.GIL.LNK.TL.
RetrocopyTLEQIANLVTSVLASPILRERLARILEHDNYIKKLLQLFHTCEDQQNTQGLHHLHDIIKGILSLNKTTLL
ParentalEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
E..FSDECIMDVVGCLEYDPALAQPK.HREFLT..AKFKEV.PITDSELR.KIHQTYRVQYI.DI.LP.P
RetrocopyEILFSDECIMDVVGCLEYDPALAQPKKHREFLTQNAKFKEVVPITDSELRKKIHQTYRVQYIYDILLPAP
ParentalSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
S.FEENFLS.LT.FIFFNKVEIVSMLQEDEKFL..VFAQL.DE.TD.DKR.EL..FFK.F.AFSQTL.P.
RetrocopySMFEENFLSSLTTFIFFNKVEIVSMLQEDEKFLFQVFAQLKDETTDNDKRLELMLFFKDFFAFSQTLEPH
ParentalNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
..D..FKTL..LGILPAL..VM.M.DLQ...AATDIF.YL.E.SPSM.R.F.MQEA....D..L.IN..I
RetrocopySKDMLFKTLTQLGILPALKMVMNMSDLQIKTAATDIFTYLMEYSPSMIRAFIMQEAEKREDEDLFINMII
ParentalEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEKG
EQ...DTDPELGGA..L.GLLR.L.DP.NML.T.N..E.SEFLNFFY.HCMH.L.APLL..TS..KC..G
RetrocopyEQIVGDTDPELGGAFHLVGLLRCLLDPDNMLITINTCERSEFLNFFYKHCMHNLIAPLLATTSGSKCGEG
ParentalRVSYLSTYDSCFYNNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCALR
.......Y.....NNYQTAQLL.LILELL.FCV.HHTY.IK.YI...DLLRRVL.L..SKHTFL.LCA.R
RetrocopyNIVGSDKYKHS-SNNYQTAQLLNLILELLIFCVQHHTYYIKHYILSNDLLRRVLMLTESKHTFLLLCAIR
ParentalFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFYKA
FMRR.IGLKDE.YNRYI..GNLFEPV..ALLDNGTRYN.LNSA.IELFE.IRVE.IKSL..H.VEN.Y..
RetrocopyFMRRMIGLKDELYNRYIIQGNLFEPVVKALLDNGTRYNMLNSAIIELFEYIRVENIKSLVVHVVEN-YNV
ParentalLESIEYVQTFKGLKTKYEQEKDRQSQKLNSVPSILRSNRFRRDAKALEEDEEMWFNEDEEEEGKAVVAPV
L.SIEYV.TFKGLK.KYEQEK.RQ.Q......S.L.S.........L...EE..FNED......AV..P.
RetrocopyLQSIEYVKTFKGLKIKYEQEKHRQNQIRENLHSMLYSKILCQGVSVLDMKEEVGFNEDMKD---AVLPPL
ParentalEKSKPEDD
E...P.DD
RetrocopyENDFPDDD

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
SRP017611_brain 0 .00 RPM 46 .36 RPM
SRP017611_kidney 0 .00 RPM 44 .80 RPM
SRP017611_liver 0 .00 RPM 20 .73 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_9 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_9 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_9 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
Bos taurus retro_btau_232
Sus scrofa retro_sscr_1187
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 ENSOCUG00000006880 1 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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