RetrogeneDB ID:

retro_nleu_2192

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397333.1:10418202..10418979(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSNLEG00000007726
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_2192
ATGTTCAAGGCGTGCCTGGTCCAGGGCTCCATCCTGAAGAAGGTGTTGGAGGCACTCAAGGACCTCATCAACGAGGCCTG
CTGGGACATCTGCTCGAGTGGTGCGAACCTGCAGAGCATGGACTCGTCGCACGTCTCCTTGGTGCAGTTGAGCCTGCTGT
CTGAGGGCTTTGACACTTACCGCTGCAACTGCAACCTGGCCATGGGGGTGAACCTCAATATTATGGCCAAAATACTAAAA
TGGGCTGGCAATGAAGATATCATTACACTAAGGACTGAAGATAACATGGATACCTTGGTGCTAGTATTTGAAGCTTCAAA
TCAGGAGAAGGTTTCAGACTATGAAATTAAGTTGATGGATTTGGATGTTGAACAAATTGGAATTGCAGAACAAGAGTACC
ACTCTGTAGTAAAGACGCCTTCTGGTGAATTTGCATGTATATACCGAGATCTCAGCCATATTGGAGATGCTGTTGTAATT
TCCTGTGTAAAAGATGGAATTAAATTTTCTGCAAGTGGAGACCTTGGAAATGGAAACAAATTGTCACAGACAAGTACTGT
CGATAAAGAGGAGGAAGATGTTACCATGGAGATGAATGAACCAGTTCAACTAACTTTTGCACTGAGGTACCTGAACTTTC
TTACAAAAGCCACTCCACTCTCTTCAATGGTGATACTCAATATGTCTGCAGAGATACACCTTGTTGTAGACTATAAAATT
GCTGATATGGGACACTTAAAGTACTACTTGGCTCCCAAGATCAAGGATGAAGAAGGA

ORF - retro_nleu_2192 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.62 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
MF.A.LVQGSILKKVLEALKDLINEACWDI.SSG.NLQSMDSSHVSLVQL.L.SEGFDTYRC..NLAMGV
RetrocopyMFKACLVQGSILKKVLEALKDLINEACWDICSSGANLQSMDSSHVSLVQLSLLSEGFDTYRCNCNLAMGV
ParentalNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMP
NL..M.KILK.AGNEDIITLR.EDN.DTL.LVFEA.NQEKVSDYE.KLMDLDVEQ.GI.EQEY..VVK.P
RetrocopyNLNIMAKILKWAGNEDIITLRTEDNMDTLVLVFEASNQEKVSDYEIKLMDLDVEQIGIAEQEYHSVVKTP
ParentalSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALR
SGEFA.I.RDLSHIGDAVVISC.KDG.KFSASG.LGNGN.KLSQTS.VDKEEE.VT.EMNEPVQLTFALR
RetrocopySGEFACIYRDLSHIGDAVVISCVKDGIKFSASGDLGNGN-KLSQTSTVDKEEEDVTMEMNEPVQLTFALR
ParentalYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEG
YLNF.TKATPLSS.V.L.MSA...LVV.YKIADMGHLKYYLAPKI.DEEG
RetrocopyYLNFLTKATPLSSMVILNMSAEIHLVVDYKIADMGHLKYYLAPKIKDEEG

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_2192 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 24 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000090891 retrocopy
retro_amel_1719,
Canis familiaris ENSCAFG000000060302 retrocopies
retro_cfam_1626, retro_cfam_946,
Callithrix jacchus ENSCJAG000000212783 retrocopies
retro_cjac_2159, retro_cjac_2175, retro_cjac_930,
Cavia porcellus ENSCPOG000000092421 retrocopy
retro_cpor_315,
Erinaceus europaeus ENSEEUG000000030691 retrocopy
retro_eeur_358,
Echinops telfairi ENSETEG000000065773 retrocopies
retro_etel_1152, retro_etel_1539, retro_etel_2217,
Felis catus ENSFCAG000000090682 retrocopies
retro_fcat_1363, retro_fcat_1729,
Homo sapiens ENSG000001326463 retrocopies
retro_hsap_3067, retro_hsap_4817, retro_hsap_857,
Gorilla gorilla ENSGGOG000000016952 retrocopies
retro_ggor_2107, retro_ggor_700,
Myotis lucifugus ENSMLUG000000016931 retrocopy
retro_mluc_1658,
Macaca mulatta ENSMMUG000000132593 retrocopies
retro_mmul_1059, retro_mmul_1960, retro_mmul_2570,
Monodelphis domestica ENSMODG000000116491 retrocopy
retro_mdom_933,
Mustela putorius furoENSMPUG000000061952 retrocopies
retro_mputfur_330, retro_mputfur_629,
Mus musculus ENSMUSG000000273421 retrocopy
retro_mmus_114,
Nomascus leucogenys ENSNLEG00000007726 2 retrocopies
retro_nleu_2192 , retro_nleu_424,
Otolemur garnettii ENSOGAG000000331612 retrocopies
retro_ogar_1258, retro_ogar_2960,
Procavia capensis ENSPCAG000000105001 retrocopy
retro_pcap_130,
Pongo abelii ENSPPYG000000107953 retrocopies
retro_pabe_2542, retro_pabe_3745, retro_pabe_690,
Pan troglodytes ENSPTRG000000132223 retrocopies
retro_ptro_2068, retro_ptro_3206, retro_ptro_595,
Pteropus vampyrus ENSPVAG000000028651 retrocopy
retro_pvam_193,
Rattus norvegicus ENSRNOG000000212641 retrocopy
retro_rnor_1035,
Sorex araneus ENSSARG000000040701 retrocopy
retro_sara_640,
Sus scrofa ENSSSCG000000306421 retrocopy
retro_sscr_113,
Tursiops truncatus ENSTTRG000000153682 retrocopies
retro_ttru_1868, retro_ttru_440,


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