RetrogeneDB ID:

retro_nleu_62

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397321.1:14454260..14455409(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSNLEG00000002917
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSNLEG00000011928
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_62
ATGGGGAGCGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTATCTCAAGGCCGCTCTGTACGTGGGTGACTTGGACCC
AGATGTCACCGAGGACATGCTCTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGATTCACCAGAATCTGCCGTGATCCGG
TGACCCGCAGCCCCCTGGGCTATGGGTATGTTAACTTCCGCTTTCCCGCGGATGCAGAGTGGGCCTTGAACACCATGAAT
TTTGATTTGATTAATGGAAAACCATTCCGCCTTATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTGGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGACAATAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGGAACATTCTGT
CCTGCAAAGTCGTATGCGATGACAACGGCTCTAAGGGTTATGCCTATGTGCACTTTGACAGCCTGGCCGCTGCCAATAGA
GCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCAGATTCAAATTCCCAGAAGAGCGGGC
GGCTGAGGTCAGAACCAGGGATAGAGCAACTTTCACCAATGTTTTCGTTAAAAACATTGGAGACGACATAGATGACGAAA
AACTGAAGGAACTTTTCTGTGAATATGGGCCAACTGAGAGTGTTAAAGTAATAAGAGATGCCAGTGGGAAATCTAAAGGC
TTTGGATTTGTGAGATACGAGACACACGAGGCTGCCCAAAAGGCTGTGCTAGACTTGCATGGAAAGTCCATCGATGGAAA
AGTCCTCTATGTAGGGCGAGCACAGAAGAAAATTGAACGCCTGGCTGAGTTGAGGCGGAGATTTGAACGGCTGAGGTTAA
AAGAAAAAAGTCGGCCCCCAGGAGTGCCTATCTATATTAAGAACTTGGATGAGACAATCAATGATGAAAAACTGAAGGAG
GAATTTTCTTCCTTTGGGTCAATTAGTCGGGCCAAAGTGATGATGGAAGTGGGGCAAGGCAAAGGATTTGGTGTGGTCTG
CTTTTCCTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGATGAATGGCCGCATAGTGGGCTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCAGGCGCAGGTGCTGA

ORF - retro_nleu_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.85 %
Parental protein coverage: 55.15 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
RetrocopyYLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI
ParentalKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
.GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
RetrocopyNGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS
ParentalQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDESLKELFSQFGK
..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KN.G...DDE.LKELF...G.
RetrocopyLAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNIGDDIDDEKLKELFCEYGP
ParentalTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQE
T.SVKV.RD.SGKSKGFGFV.YE.HE.A.KAV....GK.I.GK...VGRAQKK.ER.AEL.R.FE.L...
RetrocopyTESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKVLYVGRAQKKIERLAELRRRFERLRLK
ParentalRISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
..SR..GV..YIKNLD.TI.DEKL..EFS.FGSI..AKVM.E.G..KGFG.VCFSS.EEATKAV.EMNGR
RetrocopyEKSRPPGVPIYIKNLDETINDEKLKEEFSSFGSISRAKVMMEVGQGKGFGVVCFSSFEEATKAVDEMNGR
ParentalIVGSKPLYVALAQRK
IVGSKPL.V.L.Q..
RetrocopyIVGSKPLHVTLGQAR

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_62 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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