RetrogeneDB ID:

retro_nleu_1112

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397281.1:24841599..24843663(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSNLEG00000009338
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1112
ATGGCAGGCCTGAGGTACAGTGTAAAAGTCTTTGTCCTGAACGAAGGCCAGGAATGGAACAATCTAGGCACCGGTCAGAT
CTCATCCACCTACGACGAGCAGTTCCAGGGCATGTCGCTGCTCGTTCGGTCAGATTCAGATGGGTCAGTCATCCTGCGGT
CACGGATACCTCCAGACAGGCCCTATGGGAAATACCAAGAGACACTAATTGTTTGGTATGAAGCTGAGAACCAGGGTTTG
GTGCTACATTTCCAGGACCCAGCTGGCTGCCAGGATATTTGGGAAGAAATTTGCCAAGTTCAAGGTAAGGATACGTCTAT
CCAAACCACAGAGAACATTTCAGATGAATCAGAAGAAGACTTTAATGAAATGTCAGTAATTAGTAATACGGTTGTGCTGC
CTGACTGTGAACTCAATACACTTGAACAAATTGCTGACATAGTTACCTCGGTTCTCTCCTCACCTATTACGGATAGGGAA
AGATTGGCTGAGATCTTGAAAAATGAGGCTTATATTCCAAAACTACTGCAACTGTTCCACACTTGTGAAAACCTAGAGAA
TACTGAAGGTTTATACCATTTGCATGAAATTATCAAGGGAATTTTATCCCTCAACGAGGCATGTCTGTTTGAGATAATGT
TTTCTGACGAGTGTATCATGGATGTGGTGGGATGCCTTGAGTATGACCCTGCTTTGGATCAGCCAAAAAGGCATAGGGAC
TTCTTGACCTACGATGCAAAGTTCAAGGAAGTTATACCAATAACTAACTCTGAACTTAGGCAAAAAATACATCAGACATA
CAGATTACAGTACATTTATGACATTCTTTTGCCTGTGCCTTCCATATTTGAAGATAATTTTCTTTCTACACTTACAACTT
TTATTTTCTCCAACAAGGCTGAGATAGTAAGCATGCTGCAGAAAGATCACAAATTTTTGTATGAAGCTTTTGCACAGTTA
AAGGATGAGACTACACATGATGATAGACGGTGTGAATTGCTATGTTTTTTCAAGGAATTATGTTCATTTTCTCAGGCATT
ACAGCCTCAAAGCAGGGATGCACTATTTGAAACGTTGACACAGTTGGGAATTCTTCCTGTTCTTAAAATCGTAATGATCA
GGGATGATTTGCAAGTAAGGTCAGCTGCTGCAGTTATATGTGCTTATCTGGTGGAGTACAGTCCATCTACGATCCGAGAA
TTTATAATTTCAGAAGCTCAGGTGTGCAAAGATAGTGACCTTTTCATTAATGTAATAATTAAACAAATGATCTGTGATAC
TGATCCTGAGTTAGGAGGTGCTGTTCATTTGATGGTAATTCTCCATACTCTACTTGATCCACGCAACATGCTGACAACAC
CTGAGAAAAGTGAAAGAAGTGAATTTCTACATTTCTTCTACAAACATTGCATGCATAAATTTACAGCACCACTTTTGGCC
GCCACCTCAGAACACAACTGTGAGGAGGATGATATAGCTGGATATGACAAAAGCAAAAATTGCCCCAATGATAATCAAAC
AGCACAACTGCTTGCTTTGATATTAGAGCTACTTACATTTTGTGTACAACATCATACATACTACATAAGAAACTATATCT
TGAACAAAGACTTGCTAAGAAAGGCCTTAATATTGACAAATTCAAAGCATACTCACCTGATTTTGTGTGCTGTTCGCTTT
ATGAGAAGGATGATTGGCCTTAATGATGAAGCTTATAATAATTACATCATCAAGGGAAATCTTTTTGAGCCAGTTGTAAA
TGCTCTTCTAGATAATGGAACTCGGTACAATATGCTGAATTCAGCTATTCTTGAGCTATTTGAGTACATAAGAGTGGAAA
ATATCAAGTCTCTTGTTTCACATATAGTTGAAAAGTTTTATAACACACTTGAATCGATTGAATATGTTCAGACATTCAAA
GGATTGAAGATTAAATATGAAAAAGAGAGAGACAGACAAAGTCAAACACAAAATAATTTATATTCTGTACTGCAAAATAT
GGTAGTTTTCAGAGGTACCATAGAAGAAATTGATCTGCAAGAAGAAATATGTTTTATGGAAGAT

ORF - retro_nleu_1112 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.97 %
Parental protein coverage: 84.21 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
M...R..VKV..LNE...W...GTG..SSTY.E...GMSLLVR..SDGS..L.S.I.P...Y.K.Q.TLI
RetrocopyMAGLRYSVKVFVLNEGQEWNNLGTGQISSTYDEQFQGMSLLVRSDSDGSVILRSRIPPDRPYGKYQETLI
ParentalVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
VW.EAEN..L.L.FQ..AGC..IWE.ICQVQGKD.S...T....DESEE..F.EM...S....LP.CELN
RetrocopyVWYEAENQGLVLHFQDPAGCQDIWEEICQVQGKDTSIQTTENISDESEED-FNEMSVISNTVVLPDCELN
ParentalKLEEIADLVTSVLSSPIR-REKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATL
.LE.IAD.VTSVLSSPI..RE.LA..L.NE.YI.KLLQLF..CENLENTEGL.HL.EII.GIL.LN.A.L
RetrocopyTLEQIADIVTSVLSSPITDRERLAEILKNEAYIPKLLQLFHTCENLENTEGLYHLHEIIKGILSLNEACL
ParentalFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPT
FE.MFSDECIMDVVGCLEYDPAL.QPKRHR.FLT..AKFKEVIPIT.SELRQKIHQTYR.QYI.DI.LP.
RetrocopyFEIMFSDECIMDVVGCLEYDPALDQPKRHRDFLTYDAKFKEVIPITNSELRQKIHQTYRLQYIYDILLPV
ParentalPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQP
PS.FE.NFLSTLT.FIF.NK.EIVSMLQ.D.KFL.E.FAQL.DE.T.DD.R.EL..FFKE.C.FSQ.LQP
RetrocopyPSIFEDNFLSTLTTFIFSNKAEIVSMLQKDHKFLYEAFAQLKDETTHDDRRCELLCFFKELCSFSQALQP
ParentalQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVV
Q.RDA.F.TL..LGILP.L.IVM..DDLQVRSAA..I..YLVE.SPS..REF...EAQ...D..L.INV.
RetrocopyQSRDALFETLTQLGILPVLKIVMIRDDLQVRSAAAVICAYLVEYSPSTIREFIISEAQVCKDSDLFINVI
ParentalIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEK
I.QMICDTDPELGGAV.LM..L.TL.DP.NML.T..K.E.SEFL.FFY.HCMH..TAPLL..TSE..CE.
RetrocopyIKQMICDTDPELGGAVHLMVILHTLLDPRNMLTTPEKSERSEFLHFFYKHCMHKFTAPLLAATSEHNCEE
ParentalDNIVGSNKNHTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCAL
D.I.G..K....CP...QTAQLLALILELLTFCV.HHTY.I.NYI.NKDLLR..L.L.NSKHT.L.LCA.
RetrocopyDDIAGYDKSKN-CPNDNQTAQLLALILELLTFCVQHHTYYIRNYILNKDLLRKALILTNSKHTHLILCAV
ParentalRFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFYK
RFMRR.IGL.DE.YN.YI.KGNLFEPV.NALLDNGTRYN.LNSA..ELFE.IRVE.IKSL..HIVE.FY.
RetrocopyRFMRRMIGLNDEAYNNYIIKGNLFEPVVNALLDNGTRYNMLNSAILELFEYIRVENIKSLVSHIVEKFYN
ParentalALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSN-RFRRDAKALEEDEEMWFNED
.LESIEYVQTFKGLK.KYE.E.DRQ.Q..N...S.L.....FR.........EE..F.ED
RetrocopyTLESIEYVQTFKGLKIKYEKERDRQSQTQNNLYSVLQNMVVFRGTIEEIDLQEEICFMED

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






Nomascus leucogenys was not studied using RNA-Seq expression data.
Nomascus leucogenys was not studied using ChIP-Seq data.
Nomascus leucogenys was not studied using EST data.
Nomascus leucogenys was not studied using FANTOM5 data.
retro_nleu_1112 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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
Bos taurus ENSBTAG000000005451 retrocopy
Canis familiaris ENSCAFG000000028601 retrocopy
Equus caballus ENSECAG000000138191 retrocopy
Echinops telfairi ENSETEG000000024201 retrocopy
Felis catus ENSFCAG000000264571 retrocopy
Homo sapiens ENSG000001380411 retrocopy
Loxodonta africana ENSLAFG000000178251 retrocopy
Myotis lucifugus ENSMLUG000000038751 retrocopy
Macaca mulatta ENSMMUG000000070011 retrocopy
Mustela putorius furoENSMPUG000000024351 retrocopy
Nomascus leucogenys ENSNLEG00000009338 1 retrocopy
retro_nleu_1112 ,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
Otolemur garnettii ENSOGAG000000098371 retrocopy
Pan troglodytes ENSPTRG000000119331 retrocopy
Sus scrofa ENSSSCG000000083981 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
Tursiops truncatus ENSTTRG000000000271 retrocopy



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