RetrogeneDB ID:

retro_nleu_1517

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397297.1:8103671..8104897(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSNLEG00000019300
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSNLEG00000011928
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1517
ATGAATGTAGCAGCCAAGTACCGCATGGCCTCCCTGTATGTGGGTGACTTACATGCAGATGTCACCGAAGACCTGCTGTT
CAGGAAGTTTAGCACTGTGGGCCCTGTGCTGTCCATCCGCATTTGCAGGGACCAGGTCACCCGCCGCTCTCTGGGCTATG
CCTACGTGAACTTCTTGCAGCTGGCTGATGCCCAGAAGGCGCTGGACACAATGAACTTTGACATGATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAGCGCGATGCCTACTTGAGGAGATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAA
ATCTATCGATAACAAAACCCTTTATGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAGGTGATGAGTGATGATC
AAGGCTCCAAGGGCTATGCATTTGTGCACTTTCAGAATCAGAGTGCTGCAGACAGGGCCATTGAGGAGATGAATGGAAAA
CTACTCAAGGGCTGCAAGGTGTTTGTTGGCAGATTCAAAAACCGAAAAGATCGTGAAGCTGAACTCAGAAGCAAAGCCAG
TGAATTCACCAATATTTACATCAAAAACTTTGGAGGTGACATGGATGATGAGAGACTGAAGGACGTTTTCAGCAAATATG
GCAAAACTCTGAGTGTTAAGGTGATGACAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCAT
GAGGCTGCCAAGAAAGCTGTTGAAGAAATGAATGGAAGGGACATAAATGGGCAGCTGATTTTCGTAGGCCGGGCGCAAAA
GAAAGTAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAAAGGGAACGAATTCGTGGGTGCCAGGGGGTAA
AGCTCTATATTAAGAACCTTGATGACACCATTGATGATGAAAAACTACGAAACGAATTTTCTTCATTTGGATCAATTAGC
AGAGTTAAGGTAATGCAGGAAGAGGGGCAGAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCTGAGGATGCTACTAA
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAACCTCTTAGCATTGCTTTGGCCCAGAGACACTAGGAAAGAA
AAACGTACCTTCCCAGCTAGTATCTGCAGCAGGTGGGGGAATGATAGTGATCTCTGCCTGAACTGACCTCAGTAAATTTC
ATATTCCACATGATGGGTGCTTAGTT

ORF - retro_nleu_1517 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.29 %
Parental protein coverage: 62.12 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MN.AA..Y.MASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALD
RetrocopyMNVAAK-YRMASLYVGDLHADVTEDLLFRKFSTVGPVLSIRICRDQVTRRSLGYAYVNFLQLADAQKALD
ParentalTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFD.IKGK.IR.MWSQRD..LR.SG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GSKGY
RetrocopyTMNFDMIKGKSIRLMWSQRDAYLRRSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSKGY
ParentalAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
AFVHF..Q.AAD.AIE.MNG.LL...KVFVGRFK.RK.REAEL..KA.EFTN.YIKNFG...DDE.LK..
RetrocopyAFVHFQNQSAADRAIEEMNGKLLKGCKVFVGRFKNRKDREAELRSKASEFTNIYIKNFGGDMDDERLKDV
ParentalFSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF
FS..GKTLSVKVM.D.SGKSKGFGFVS...HE.A.KAVEEMNG..I.G..IFVGRAQKKVERQAELK..F
RetrocopyFSKYGKTLSVKVMTDSSGKSKGFGFVSFDSHEAAKKAVEEMNGRDINGQLIFVGRAQKKVERQAELKQMF
ParentalEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
EQLK.ERI...QGV.LYIKNLDDTIDDEKLR.EFS.FGSI...KVM.E.G.SKGFG..CFSSPE.ATKA.
RetrocopyEQLKRERIRGCQGVKLYIKNLDDTIDDEKLRNEFSSFGSISRVKVMQEEGQSKGFGLICFSSPEDATKAM
ParentalTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRV-AGMRALPANAILNQFQPAAGGYFV
TEMNGRI.GSKPL..ALAQR..ERK..L...Y.Q.V..GM....A...L..F.....G..V
RetrocopyTEMNGRILGSKPLSIALAQRH*ERKTYLPS*YLQQV<GGMIVISA*TDLSKFHIPHDGCLV

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_1517 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 20 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Nomascus leucogenys ENSNLEG00000011928 2 retrocopies
retro_nleu_1517 , retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,


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