RetrogeneDB ID:

retro_nleu_611

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397268.1:9016605..9018304(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC1
Ensembl ID:ENSNLEG00000003142
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_611
GCTTTGGACACCATGAATTTTGATTTTATAAAGGGCAAGTCAGTACGCATCACGTGGTCTCAGCCTGAACCATCACTTCG
CAGTCGAGTGGGCAACATATTCATTAAAAATCTGGACAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGATT
TTTGTAACATCGTTTCATGTAAAGTGGTTTGTGATGAAAATGGTGCCAGGGGCTATGGATTTGTACGCTTTGATATGCAC
GGAGCAGCTGAAAGAGCTCTTGAAAAAATGAATGGAATGCTCCTAAACGGTCGCAAAGTATTTGTTGGACGATTTAAGTC
TCGTAAAAAACGAGAAACTGAACTTGGAGCTAAGGTAAAAGAGTTCACCAATGTTTACAAGAATTTTGGAGGAGACATGG
ATGATGAGCGCCTTAAGGATCTCTTTGACAAGTTTGGGCCTGCCGTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAA
TCCGAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAGATGCACCGAAAGCTGTGGATTAGATTAATGGAAATGGAGCT
CAATGGAAAACGAATTTACGTTAGTCGAGCTCAGAAAAAGGTGGAACAGCAGACGGAACTTTAGCGCAAATTCGAACAGA
TGAAGCAAGATAGGATTACCAGGTACTAGGGTGTTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGT
CTCTGGAAACATTTTCTCCATTTGGTACAATCACCAGTCCAAAGGTTATGATGGAGGGTGGTCGCAGCAAGGGTTTGGTT
TTGTATGTTTCTCCTCCCCAGAAGAAGCCACAAAAGCAGTTACAGAAACGAATGGTAGAATTGTGGTCACAAAGCCATTG
TATGTAACTTTAGCTCAGCGCAAGGGAGAGTGCCAGGCTCACTTCACTAACCAGTATATGCAGAGAATGGCAAGTGTATG
AGCTGTGCCCAACCCTGTAATCAACCCTTACCAGCTAGCGTCTCCTTCAGGTTTCTTAATGGCAGCTATCTCACAGTCTC
AGAACTGTGCTGCATACCATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGA
CCTCATCCATTCCAAAATATGCCCGGTGCTACCCACCCAGCTGCTCCTAGGCCACCATTTAGTACTATGAGACCAGCTTC
TTCACAGGTTCCACGAGTCATGTCAACACAGTGTGCTGCTAACACATCAACACGGACAATGGGTCCACATCCTGCAGCTG
CAGCTGCTGCAGCTACTCCTGCTGTCTGCACCATTCCACAGTATAAATATGGTGCGGGATTTCGCAATCCTCAGCAACAT
CTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTGCTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTT
GGCATCTGCCCGTCCTCAAGAGGAAAAGCAAATGTTGGGTGAGTGGCTATTTCCTTTTATTCAAGCCACGCACCCTACTC
TTGCTAGTAAAATCACTGGCATATTGTTGGAGATTGATAATTCAGAACTTCTTCATATGCTTGAGTCTCCAGAGTCACTC
CGTTATAAGGTTGATGAAGCTGTAGCTATACTACAAGCCCATCAAGCTAAAGAGGCTTCCCAGAAAGCAGTTAGCAGCAC
CACTGGTGTTCCAACTGTT

ORF - retro_nleu_611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.69 %
Parental protein coverage: 89.47 %
Number of stop codons detected: 4
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS
ALDTMNFD.IKGK.VRI.WSQ..PSLR.S.VGNIFIKNLDKSIDNKALYDTFS.F.NI.SCKVVCDENG.
RetrocopyALDTMNFDFIKGKSVRITWSQPEPSLR-SRVGNIFIKNLDKSIDNKALYDTFSDFCNIVSCKVVCDENGA
ParentalKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERL
.GYGFV.F....AAERA.EKMNGMLLN.RKVFVGRFKSRK.RE.ELGA..KEFTNVY.KNFG.DMDDERL
RetrocopyRGYGFVRFDMHGAAERALEKMNGMLLNGRKVFVGRFKSRKKRETELGAKVKEFTNVY-KNFGGDMDDERL
ParentalKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHE-DAQKAVDEMNGK-ELNGKQIYVGRAQKKVERQTE
KDLF.KFGPA.SVKVMTDESGKS.GFGFVSFERHE.DA.KAVD..NG..ELNGK.IYV.RAQKKVE.QTE
RetrocopyKDLFDKFGPAVSVKVMTDESGKSEGFGFVSFERHE<DAPKAVD*INGN>ELNGKRIYVSRAQKKVEQQTE
ParentalLKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEF-SPFGTITSAKVMMEGGRSKG-FGFVCFSSP
L.RKFEQMKQDRITRY.GVNLYVKNLDDGIDDERL.K.F.SPFGTITS.KVMMEGGRSKG.FGFVCFSSP
RetrocopyL*RKFEQMKQDRITRY*GVNLYVKNLDDGIDDERLWKHF<SPFGTITSPKVMMEGGRSKG<FGFVCFSSP
ParentalEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAI
EEATKAVTE.NGRIV.TKPLYV.LAQRK.E.QAH.TNQYMQRMASV.AVPNPVINPYQ.A.PSG..MAAI
RetrocopyEEATKAVTETNGRIVVTKPLYVTLAQRKGECQAHFTNQYMQRMASV*AVPNPVINPYQLASPSGFLMAAI
ParentalPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVA
.Q.QN.AAY.PPSQIAQLRPSPRWTAQGARPHPFQNMPGA..PAAPRPPFSTMRPASSQVPRVMSTQ..A
RetrocopySQSQNCAAYHPPSQIAQLRPSPRWTAQGARPHPFQNMPGATHPAAPRPPFSTMRPASSQVPRVMSTQCAA
ParentalNTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA
NTST.TMGP.PAAAAAAATPAV.T.PQYKY.AG.RNPQQHLNAQPQVTMQQPA.HVQGQEPLTASMLASA
RetrocopyNTSTRTMGPHPAAAAAAATPAVCTIPQYKYGAGFRNPQQHLNAQPQVTMQQPAAHVQGQEPLTASMLASA
ParentalPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAA
.PQE.KQMLGE.LFP.IQA.HPTLA.KITG.LLEIDNSELLHMLESPESLR.KVDEAVA.LQAHQAKEA.
RetrocopyRPQEEKQMLGEWLFPFIQATHPTLASKITGILLEIDNSELLHMLESPESLRYKVDEAVAILQAHQAKEAS
ParentalQKAVNSATGVPTV
QKAV.S.TGVPTV
RetrocopyQKAVSSTTGVPTV

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_611 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 15 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG00000003142 3 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611 ,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,


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