RetrogeneDB ID:

retro_nleu_1510

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397297.1:4088069..4088905(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ENSG00000232856
Ensembl ID:ENSNLEG00000003528
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1510
CTGGCTGACATCGCAGTTTTCTGCACCCTGTTGTGGCTCTATAAGCAGGTTCTGGAGCCTTCTTCCTGCCGGGCCTTTCC
CAATACCAACCGCTGGTTCCTCACCTGCATTAACCAGCCACAATTCCGGGCTGTCTTAGGGAAGGTGAAACTGTCTGAGA
ACATGACCCAGTTTGATGCTAAAAAGCTTGCAGAAAGCCAGCCTGAAAAAGACACCCCATGGAAAGGGAAAGTTTCACGG
GAAAAGAAACAGTAGCCCCAGGCTGAGCGGAAGGAGGAGAAAAAGGCGGCTGCCCCTGCTCCTGAGGAGGAGATGGACGA
ATGTGAGCAGGTGCTGGCTGCTGAGCTCAAGGTCAAAGACCTCTTCGCTCACTTACTCAAGAGTTCCTTTGTGTTGGATG
AATTTAAGCGCAAGTACTCCAACGAGGACACACTCTCTGTGGCGCTGCCCTATTTCTGGGAGCACGTTGATAAGGATGGC
TGGTCCCTGTGGTACTCACAATATCGCTTTCCTAAAGAACTCACTCAGACCTTTATGACTTGCAATCTCATCACTGGAAT
GTTCAAGCGACTGGACAAGCTAAGGAAGATGCCTTTGCCAGTGTCATCCTCTTTGGAACCAACAACAGCAGCTCTGTTTC
TGGAGTCTGGGGCTTCTGAGGCCAGGAGCTTGCATTTCTGCTGAGTCCAGATTGGCAGATGGACTACCAGTCATACACAC
GGCAAAAACCGGCTCCTGGCAGCGAGGAGCCCCAGACCCTGGTTGGAGCGTACTTTTCCTGGGAGGAGGGCTTCCAGAAT
ATGGGCAAAGCCTTCAATCAGGACGAGATCGTCAAG

ORF - retro_nleu_1510 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.79 %
Parental protein coverage: 57.29 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAETQPKK
LADI.V.CTLLWLYKQVLEPS...AFPNTNRWFLTCINQPQFRAVLG.VKL.E.M.QFDAKK.AE.QP.K
RetrocopyLADIAVFCTLLWLYKQVLEPSSCRAFPNTNRWFLTCINQPQFRAVLGKVKLSENMTQFDAKKLAESQPEK
ParentalDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKYS
DTP.K.K.SRE.KQ.PQAERKEEKKAAAPAPEEEMDECEQ.LAAE.K.KD.FAHL.KS.FVLDEFKRKYS
RetrocopyDTPWKGKVSREKKQ*PQAERKEEKKAAAPAPEEEMDECEQVLAAELKVKDLFAHLLKSSFVLDEFKRKYS
ParentalNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLDKLRK-NAFASVILFGTNN
NEDTLSVALPYFWEH.DKDGWSLWYS.YRFP.ELTQTFM.CNLITGMF.RLDKLRK..AFASVILFGTNN
RetrocopyNEDTLSVALPYFWEHVDKDGWSLWYSQYRFPKELTQTFMTCNLITGMFKRLDKLRK<DAFASVILFGTNN
ParentalSSSISGVWVFRGQELAFPLNPDWQVDYESYTWRKLDPGSEETQTLVREYFSWEGAFQHVGKAFNQGKIFK
SSS.SGVW.F.GQELAF.L.PDWQ.DY.SYT..K..PGSEE.QTLV..YFSWE..FQ..GKAFNQ..I.K
RetrocopySSSVSGVWGF*GQELAFLLSPDWQMDYQSYTRQKPAPGSEEPQTLVGAYFSWEEGFQNMGKAFNQDEIVK

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_1510 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 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000067451 retrocopy
retro_amel_772,
Bos taurus ENSBTAG000000118431 retrocopy
retro_btau_1600,
Canis familiaris ENSCAFG000000158346 retrocopies
retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus ENSCJAG000000189496 retrocopies
retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus ENSECAG000000143341 retrocopy
retro_ecab_419,
Erinaceus europaeus ENSEEUG000000012311 retrocopy
retro_eeur_575,
Homo sapiens ENSG000002547724 retrocopies
retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Latimeria chalumnae ENSLACG000000147001 retrocopy
retro_lcha_82,
Loxodonta africana ENSLAFG000000033391 retrocopy
retro_lafr_381,
Myotis lucifugus ENSMLUG000000003421 retrocopy
retro_mluc_1110,
Macaca mulatta ENSMMUG000000065985 retrocopies
retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica ENSMODG000000076911 retrocopy
retro_mdom_68,
Mustela putorius furoENSMPUG000000139422 retrocopies
retro_mputfur_427, retro_mputfur_944,
Mus musculus ENSMUSG000000716447 retrocopies
retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys ENSNLEG00000003528 2 retrocopies
retro_nleu_1510 , retro_nleu_681,
Oryctolagus cuniculus ENSOCUG000000209593 retrocopies
retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Otolemur garnettii ENSOGAG000000008271 retrocopy
retro_ogar_1344,
Ochotona princeps ENSOPRG000000145631 retrocopy
retro_opri_814,
Pongo abelii ENSPPYG000000294345 retrocopies
retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes ENSPTRG000000037683 retrocopies
retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus ENSPVAG000000034401 retrocopy
retro_pvam_1239,
Rattus norvegicus ENSRNOG000000200758 retrocopies
retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus ENSSARG000000112321 retrocopy
retro_sara_718,
Sus scrofa ENSSSCG000000130641 retrocopy
retro_sscr_164,
Ictidomys tridecemlineatus ENSSTOG000000028512 retrocopies
retro_itri_852, retro_itri_886,
Tursiops truncatus ENSTTRG000000024593 retrocopies
retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,


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