RetrogeneDB ID:

retro_nleu_1024

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397279.1:3127258..3129566(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATMIN
Ensembl ID:ENSNLEG00000010465
Aliases:None
Description:ATM interactor [Source:HGNC Symbol;Acc:29034]


Retrocopy-Parental alignment summary:






>retro_nleu_1024
GCGACGCAGCAGCCCGCGGCCCCCGTGCTGGCGGGGATGCTGATCCAGCAGTAGGTGAGCGAGCTGTCCCAGGCCGTGTG
GACCAACATCCTGTGCACCGTGCGCGGCTGCCGCAAGATCCTGCCCAACAGCCACGCGCTCAACATGCACCTGGTCAAGA
GCCACCGCCTGCAGGATAGCATAGTCAATTCAACAATAAGAAAAGATTTGAAAACTATACCGAAATTCTACTGTTGTCCA
ATCGAAGGCTGACCCAGAGGCCCTGACAGACCATTTTCTCAGTTTTCTCTCGTAAAACAGCACTTCTGAAAATGCATGCT
GAGAAGAAGCACAAATGTAGTAAGTGCAGCAATTCGTACGGTACAGAATGGGACCTGAAAAGACACGCAGAGGACTGTGG
CAAGACCTTCCGGTGCACATGCGGCTGTCCCTACGCCAGTAGAACAGCATTGCAGTCTCACATCTACCGAACTGGCCACG
AGATCCCTGCAGAACACAGGGACCCACCTAGTAAGAAAAGGAAAATGGAAAACTGTGCAAAACCAGAAGCTATCCAACAA
GACCACTGAATCATTTAACAACCAACCAATCAATCCCTAGACCAGACACTCAAGAACTAGAAGCTTCAGAAATAACGCTA
GAACCATCTTTTGAAGACTCTTGTGGCTCTAACACTGACAGGCAGACTCTTACAACACCACCGAGATATCCTCAGAAGTT
GCTTTTACCAAAGCCCAAAGTGGCTTTGCTTAAACTACCCGTGATGCAGTTTTCCCTCATGCCTGTCTTTGTGCCTACAG
CCGACTCCTCAGCCCAGCCTGTGCTGTTAGGTGTCGATCAGGGCTCTGCCACAGGGGCTGTGCAGTTACCGCCCTTGTCA
GTAGGAACCCTGATCCTTGGCCTAGATTCAGAGGCTTGCTCTCTTAAGGAGAGCCTACCTCTTTCCTAAATTGCTGATCC
TGCTGCTGTTGAGCCAATAAGTACTGGTGTTCAAGTGAACTTGGGTAAAAGTCCATCTAATCCTTTACAAGAACTAAGGA
ACACATGTCAAAAGAACAGCATTTCTTCAATCAATGTGCAGACAGATCTGTCTTATGCCTCACAAAACTTTATACCTTCT
GCACAGTGGGCCACCACTGATTCCTCTGTGTCGTCTTGTTCTCAAACTGATTTGTTGTTTGATTCTCAAGTGTCTCTTCC
CATTAGTGTTCACACTCAGACATTTTTGCCCAGCTCTAAGGTAACTTCATCTATAGCTGCTCAGACTGATGCATTTATGG
ACACCTGTTTCCAGTCGGGTGGGGTCTCCAGAGAAACTCAAACCAGTGGGATACGAAGTCCAACAGATGACCATGTACAG
AAGGACCAAGCTGGAATGTGCGGAGACATTTTTGAGAGTGTTCATTCATCATATAATGTTAATACAAGTAACATTATAAG
CAACAGTTTAGTAGCAGAGACAGTAACTCATAGTTTGTTACCTCAGAATGAGCCTAAGACTTTAAATCAAGATATTGAGA
AATGTGCACCAATTATAAACTTCAGTGCACAGAATAGTATGCTTCCTTTACAGAACATGACAGATAATCAGACCCAAACC
ACAGATTTATTAAATGATTTGGAAAACATCTTGTCAAGTAATCTGCCTGCTCAGACACTGGATCATCGTAGTCTTTTGTC
TGACAGAAATCCTGGACCTGACACCCAGCTCCCATCTGGCCCAGCCCAGAACCCTGGAATCAATTTTAATATCGAAGAGT
TCTTTTTGGCCTCACATATCCAGACTCAAACTGAAGAGAATGAACTTAGCACCATGAACAACGAGCCAGTCTTGGAGTCA
CTGGACATAGAGACTCAAACGGACTTCTTACTCGCAGATACCTCTGCTCAGTCCTACGGGTGTAGGGGAAATTCTAACTT
CTTAGGCCTTGAGATGTTTGACACACAGACACAGACAGACTTAAACTTTTTCTTAGACAGTAGTCCTCATCTGCCTCTGG
GAAGTATTCTGAAACACTCCAGCTTTTCCATGAGTACTGATTCATCTGACACAGAGACCCAAACTGAAAGAATCTCCACT
GCTAAAAATATACCTGCTCTAGAAAGCAAAGTTCAGTTGAACAGTATAGAAACACAGACCATGAGTTCTGGGTTTGAAAC
CCTGGGGAGCTTGTTCTTCACCAGCAACGAAACACAAACAGCAATGGACGACTTTCTTCTGGCTGATATGGCCTGGAACA
TGATGGAGTCTCAGTTCAGCTCTGTAGAAACCCAGACTTCTGCGGAACCACACACAGTCTCCAACTTC

ORF - retro_nleu_1024 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.87 %
Parental protein coverage: 99.87 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalATQQPAVPAPPAGELIQPSVSELSRAVRTNILCTVRGCGKILPNSPALNMHLVKSHRLQDGIVNPTIRKD
ATQQPA.P...AG.LIQ..VSELS.AV.TNILCTVRGC.KILPNS.ALNMHLVKSHRLQD.IVN.TIRKD
RetrocopyATQQPAAPVL-AGMLIQQ*VSELSQAVWTNILCTVRGCRKILPNSHALNMHLVKSHRLQDSIVNSTIRKD
ParentalLKTGPKFYCCPIEGCPRGPERPFSQFSLVKQHF-MKMHAEKKHKCSKCSNSYGTEWDLKRHAEDCGKTFR
LKT.PKFYCCPIEG.PRGP.RPFSQFSLVKQHF..KMHAEKKHKCSKCSNSYGTEWDLKRHAEDCGKTFR
RetrocopyLKTIPKFYCCPIEG*PRGPDRPFSQFSLVKQHF<LKMHAEKKHKCSKCSNSYGTEWDLKRHAEDCGKTFR
ParentalCTCGCPYASRTALQSHIYRTGHEI-PAEHRDPPSKKRKMENCAQNQKLSNKTIESLN-NQPIPRPDTQEL
CTCGCPYASRTALQSHIYRTGHEI.P.....P.......................L..NQ.IPRPDTQEL
RetrocopyCTCGCPYASRTALQSHIYRTGHEI<PCRTQGPT**EKENGKLCKTRSYPTRPLNHLTTNQSIPRPDTQEL
ParentalEASEIKLEPSFEDSCGSNTDKQTLTTPPRYPQKLLLPKPKVALVKLPVMQFSLMPVFVPTADSSAQPVVL
EASEI.LEPSFEDSCGSNTD.QTLTTPPRYPQKLLLPKPKVAL.KLPVMQFSLMPVFVPTADSSAQPV.L
RetrocopyEASEITLEPSFEDSCGSNTDRQTLTTPPRYPQKLLLPKPKVALLKLPVMQFSLMPVFVPTADSSAQPVLL
ParentalGVDQGSATGAVHLLPLSVGTLILGLDSEACSLKESLPLFKIANPIAGEPISTGVQVNFGKSPSNPLQELG
GVDQGSATGAV.L.PLSVGTLILGLDSEACSLKESLPL..IA.P.A.EPISTGVQVN.GKSPSNPLQEL.
RetrocopyGVDQGSATGAVQLPPLSVGTLILGLDSEACSLKESLPLS*IADPAAVEPISTGVQVNLGKSPSNPLQELR
ParentalNTCQKNSISSINVQTDLSYASQNFIPSAQWATADSSVSSCSQTDLSFDSQVSLPISVHTQTFLPSSKVTS
NTCQKNSISSINVQTDLSYASQNFIPSAQWAT.DSSVSSCSQTDL.FDSQVSLPISVHTQTFLPSSKVTS
RetrocopyNTCQKNSISSINVQTDLSYASQNFIPSAQWATTDSSVSSCSQTDLLFDSQVSLPISVHTQTFLPSSKVTS
ParentalSIAAQTDAFMDTCFQSGGVSRETQTSGIESPTDDHVRMDQAGMCGDIFESVHSSYNVATGNIISNSLVAE
SIAAQTDAFMDTCFQSGGVSRETQTSGI.SPTDDHV..DQAGMCGDIFESVHSSYNV.T.NIISNSLVAE
RetrocopySIAAQTDAFMDTCFQSGGVSRETQTSGIRSPTDDHVQKDQAGMCGDIFESVHSSYNVNTSNIISNSLVAE
ParentalTVTHSLLPQNEPKTLNQDIEKSTPIINFSAQNSMLPSQNMTDNQTQTIDLLSDLENILSSNLPAQTLDHR
TVTHSLLPQNEPKTLNQDIEK..PIINFSAQNSMLP.QNMTDNQTQT.DLL.DLENILSSNLPAQTLDHR
RetrocopyTVTHSLLPQNEPKTLNQDIEKCAPIINFSAQNSMLPLQNMTDNQTQTTDLLNDLENILSSNLPAQTLDHR
ParentalSLLSDTNPGPDTQLPSGPAQNPGIDFDIEEFFSASNIQTQTEESELSTMNTEPVLESLDIETQTDFLLAD
SLLSD.NPGPDTQLPSGPAQNPGI.F.IEEFF.AS.IQTQTEE.ELSTMN.EPVLESLDIETQTDFLLAD
RetrocopySLLSDRNPGPDTQLPSGPAQNPGINFNIEEFFLASHIQTQTEENELSTMNNEPVLESLDIETQTDFLLAD
ParentalTSAQSYGCRGNSNFLGLEMFDTQTQTDLNFFLDSSPHLPLGSILKHSSFSMSTDSSDTETQTEGISTAKN
TSAQSYGCRGNSNFLGLEMFDTQTQTDLNFFLDSSPHLPLGSILKHSSFSMSTDSSDTETQTE.ISTAKN
RetrocopyTSAQSYGCRGNSNFLGLEMFDTQTQTDLNFFLDSSPHLPLGSILKHSSFSMSTDSSDTETQTERISTAKN
ParentalIPALESKVQLNSTETQTMSSGFETLGSLFFTSNETQTAMDDFLLADLAWNTMESQFSSVETQTSAEPHTV
IPALESKVQLNS.ETQTMSSGFETLGSLFFTSNETQTAMDDFLLAD.AWN.MESQFSSVETQTSAEPHTV
RetrocopyIPALESKVQLNSIETQTMSSGFETLGSLFFTSNETQTAMDDFLLADMAWNMMESQFSSVETQTSAEPHTV
ParentalSNF
SNF
RetrocopySNF

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_1024 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Nomascus leucogenys ENSNLEG00000010465 1 retrocopy
retro_nleu_1024 ,
Rattus norvegicus ENSRNOG000000114221 retrocopy
retro_rnor_2526,


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