RetrogeneDB ID:

retro_nleu_1610

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397301.1:1035921..1037582(+)
Located in intron of:ENSNLEG00000027013
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IPO5
Ensembl ID:ENSNLEG00000007831
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1610
CAGGATCCTCATCCAAGGGTGAGGGCTCCAGCCTGTACTATACTTGGATAGATGGCACAGATTTTGCACCTAATTTCCAA
AAGAAATTTCATGAAACAGTGATTCTAGCTTTGTTACGTACCATGCAAAATCAAGGTAATCAGCATGTGCAATCACATGC
AGCTTCTGCTCTTACTGTTTTTATTGAAGACTGCCCCAAATCATTTCTAGTTCTATATTTGGATAGTATGGTGAGAAACC
TACATTCTGTCTTGGTGATTAAGCTTCAAGAGTTGATTCGGAACGGAACTAATTTGGCCCTGGAATAACTTGTTGCAACC
ATTGCATCGGTTGCAGATACAACAGAAGAAAAATTTGTCCCATATTATGATATATTCATGCCCTCACTAAAGCACATCAT
TGAGCTTGCTGTTCAGAAGGAACTCAAGCTTCTGAGAGGAAAAACTATTGTGTGCATTAGCCATATTGGTCTTGCTGTTG
TGAAGAAAAAATTTATGCAAGATGCATCAAATGTGATGTAGCTCTTGTTGAAGACACAATCAGACTTAAATATTATGGAA
GATAATGACCCTCAGACCTCTTACATGGTTTCAGCATGGGCTAGAACCTGTAAAATTCTTGGAAAAGATTTTCAACAGTA
CCTTTCACTGGTTATCGAGCCTCTTATTAAGACTGCTTCAGCTAAACCTGATGCTGCTCTCTCAGACACCCAGGATGTGG
AGAATATGAGTGATGATGACGGCTGGCAATATGTAAATCTTGGAGACCAACAGTGTTTTGGACTTAATACTTCAGGACTT
GAAGCAAAAGTAACTGCTTGCCAGATGTTGGTTTACTATGCTAAGGAGTTAAGGGAAGGGTTTGTGAACTATACAGAATA
AGTTGTGAAGCTGATGGTTCCTTTACTGAAATTTTATTTCCATGACAATGTTGGAGTGGGAGCAGCACAGTCCATGCCTT
TTCTCCTGGAATGTGCAAGAATCTGTGGCCCAGAGTATCTTGCACAGATGTGGCAATTCATACGTAACCCCTTAATCAAG
GCTACTGGTACTGAACCAGATACAGATGTGCGCTCAGAAATAATGAATTCTTTTGCAAAGTTCATTGAAGTTATGGGAGA
TGATTGCCTTAATGATGAATACTTGGAAGAACTGGGAGGAATACTGAGAGCAAAACTTGAAGGGCACTTTAAAAATGAAG
AATTGTGACAGGTTAAAAGACAGAAAGAAAACTATGATCAAAAGGTTGAGATATCTCCACAAGATGAGGATGAATGTGAT
GTTTATATTCTGACTGAAGTATCAGATATTTTGCACACATTATTTAGTACTTATAAGGAAAAGATTTTACCATGATTTGA
ACAACTACTTCCATTAATTGTAAATCTAATTTGTTCAAGTAGGCCATGGCTAGGCAGACAGTGGGGATTGTGCATATTTG
ATGACATCACAGAACACTGCAGTCCAACTTCATTTAAATATGTAGACTATTTTCGGTGGCCAATGCTACTAAATATGTGA
GATAACAATCCTGAAGTCAGGCAAGCTGCTGCTTATGGTCTGGGTGTCATGGCACAGCTTAGTGGAGATGATTATCGTTC
TTTATGTTCAGAAGCTGTCCCACTGCTGGTAAAAGTTATTAAGTGGGCAAATTCCAAAACC

ORF - retro_nleu_1610 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.69 %
Parental protein coverage: 51.82 %
Number of stop codons detected: 7
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQDPHPRVRYAACNAVGQMA-TDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSL
QDPHPRVR..AC...G.MA.TDFAP.FQKKFHE.VI.ALL.TM..QGNQ.VQ.HAA.AL..F.EDCPKS.
RetrocopyQDPHPRVRAPACTILG*MA<TDFAPNFQKKFHETVILALLRTMQNQGNQHVQSHAASALTVFIEDCPKSF
ParentalLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQ
L..YLD..V..LHS..V.KLQELI..GT.L.LE..V..IASVADT.EEKFVPYYD.FMPSLKHI.E.AVQ
RetrocopyLVLYLDSMVRNLHSVLVIKLQELIRNGTNLALE*LVATIASVADTTEEKFVPYYDIFMPSLKHIIELAVQ
ParentalKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTDFNDMEDDDPQISYMISAWARMCKILGK
KEL.LLRGKTI.CIS.IGLAV.K.KFMQDAS.VM.LLLKTQ.D.N.MED.DPQ.SYM.SAWAR.CKILGK
RetrocopyKELKLLRGKTIVCISHIGLAVVKKKFMQDASNVM*LLLKTQSDLNIMEDNDPQTSYMVSAWARTCKILGK
ParentalEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVC
.FQQYL..V..PL.KTAS.KP..AL.DTQD.ENMSDDDGW..VNLGDQQ.FG..T.GLE.K.TACQMLV.
RetrocopyDFQQYLSLVIEPLIKTASAKPDAALSDTQDVENMSDDDGWQYVNLGDQQCFGLNTSGLEAKVTACQMLVY
ParentalYAKELKEGFVEYTEQVVKLMVPLLKFYFHDGVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAI
YAKEL.EGFV.YTE.VVKLMVPLLKFYFHD.V.V.AA.SMP.LLECAR..GPEYL.QMW.F....LIKA.
RetrocopyYAKELREGFVNYTE*VVKLMVPLLKFYFHDNVGVGAAQSMPFLLECARICGPEYLAQMWQFIRNPLIKAT
ParentalGTEPDSDVLSEIMHSFAKCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEES
GTEPD.DV.SEIM.SFAK.IEVMGD.CLN.E..EELGGIL.AKLE.HFKN.EL.QVKRQ.E.YD..VE.S
RetrocopyGTEPDTDVRSEIMNSFAKFIEVMGDDCLNDEYLEELGGILRAKLEGHFKNEEL*QVKRQKENYDQKVEIS
ParentalLQDEDDNDVYILTKVSDILHSIFSSYKENVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSP
.QDED..DVYILT.VSDILH..FS.YKE..LP.FEQLLPLIVNLIC..RPW..RQWGLCIFDD..EHCSP
RetrocopyPQDEDECDVYILTEVSDILHTLFSTYKEKILP*FEQLLPLIVNLICSSRPWLGRQWGLCIFDDITEHCSP
ParentalASFKYAEYFLRPMLQYVCDNSPEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKT
.SFKY..YF..PML....DN.PEVRQAAAYGLGVMAQ..GD.YR..C.EA.PLLV.VI..A.SKT
RetrocopyTSFKYVDYFRWPMLLNM*DNNPEVRQAAAYGLGVMAQLSGDDYRSLCSEAVPLLVKVIKWANSKT

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






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_1610 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 21 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG000000393741 retrocopy
retro_btau_104,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG000000060611 retrocopy
retro_chof_11,
Cavia porcellus ENSCPOG000000048272 retrocopies
retro_cpor_265, retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG000000161901 retrocopy
retro_lafr_22,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG000000306622 retrocopies
retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys ENSNLEG00000007831 2 retrocopies
retro_nleu_1610 , retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,


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