RetrogeneDB ID:

retro_nleu_74

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397271.1:36057175..36058342(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSNLEG00000018620
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSNLEG00000009805
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_74
ATGCTGGCTGCCTTCATCTCCCGCGTGTTGAGGCGAGTTGCCCAGAAATCAGCTCGCAGAGTGCTGGTGGCATCCCGTAA
CTCCTCAAATGACGCTACATTTGAAATTAAGCAATGTGATCTTTATCTGTTGGAAGAGGGTCCCCCTGTCACTACAGTGC
TCACTAGGGCGGAGGGGCTTAAATACTACAGGATGATGCTGACTGTTCGCCGCATGGAATTGAAGGCAGATCAGCTGTAC
AAACAGAAATTCATTCGCGGTTTCTGTCACCTGTGTGATGGTCAGGAAGCCTGCTGCGTGGGCCTTGAGGCCGGCATAAA
CCCCTCGGACCACGTCATCACATCATATAGGGCTCATGGTGTGTGCTATACTCGGGGGCTTTCTGTCCGATCCATTCTCG
CAGAGCTGACGGGAAGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGATCGATGCATATGTATACCAAGAACTTCTACGGG
GGCAATGGCATCGTTGGTGCGCAGGGCCCCCTGGGCGCTGGCATTGCTCTGGCCTGTAAATATAAAGGAAACGATGAGAT
CTGTTTGACTTTATATGGGGATGGGGCTGCGAATCAGGGGCAGATGGCCGAAGCTTTCAATATGGCAGCTTTATGGAAAT
TACCTTGTGTTTTCATCTGTGAGAATAACCTATATGCAATGGGAACATCTACTGAGAGAGCAGCAGCCAGCTCTGATTAC
TACAAGAGGGGCAATTTTATCCCTGGGCTAAAGGTCGATGGAATGGATGTTCTGTGTGTTCGTGAGGCAACAAAATTTGC
AGCCGACTACTGTAGATCTGGAAAGGGGCCCATACTGATGGAGCTGCAGACCTACCGTTTTCATGGACACAGTATGAGTG
ATCCTGGAGTCAGTTATCGTACACGAGAAGAAATTCAGGAAGTAAGAAGTAAGAGGGATCCTATAATGATTCTCCAAGAT
AGAATTGTAAGCAGCAAGCTCGCCACTGTGGAAGAATTAAAGGAAATTGGGACTGAGGTGAGGAAAGAAATTGATGATGC
TTCCCAGTTTGCTACCACTGATATTGAGCCACATTTGGAAGAATTAGGCCATCACATCTACAGCAGTGATTCATCTTTTG
AAGTTCGTGGTGCAAATCCATGGATCAAGTTTAAGTCCGTCAGTTAA

ORF - retro_nleu_74 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.02 %
Parental protein coverage: 99.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLAA-VSRVLSGASQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVR
MLAA..SRVL....QK.A.RVLVASRN..NDATFEIK.CDL..LEEGPPVTTVLTR..GLKYYRMM.TVR
RetrocopyMLAAFISRVLRRVAQKSARRVLVASRNSSNDATFEIKQCDLYLLEEGPPVTTVLTRAEGLKYYRMMLTVR
ParentalRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRK
RMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGINP.DH.IT.YRAHG...TRGLSVR.ILAELTGR.
RetrocopyRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPSDHVITSYRAHGVCYTRGLSVRSILAELTGRR
ParentalGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAA
GGCAKGKGGSMHMY.KNFYGGNGIVGAQ.PLGAGIALACKY.G.DE.CLTLYGDGAANQGQ..EA.NMAA
RetrocopyGGCAKGKGGSMHMYTKNFYGGNGIVGAQGPLGAGIALACKYKGNDEICLTLYGDGAANQGQMAEAFNMAA
ParentalLWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILM
LWKLPC.FICENN.Y.MGTS.ERAAAS.DYYKRG.FIPGL.VDGMD.LCVREAT.FAA.YCRSGKGPILM
RetrocopyLWKLPCVFICENNLYAMGTSTERAAASSDYYKRGNFIPGLKVDGMDVLCVREATKFAADYCRSGKGPILM
ParentalELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQF
ELQTYR.HGHSMSDPGVSYRTREEIQEVRSK.DPIM.L.DR.V.S.LA.VEELKEI..EVRKEI.DA.QF
RetrocopyELQTYRFHGHSMSDPGVSYRTREEIQEVRSKRDPIMILQDRIVSSKLATVEELKEIGTEVRKEIDDASQF
ParentalATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS
AT.D.EP.LEELG.HIYSSD..FEVRGAN.WIKFKSVS
RetrocopyATTDIEPHLEELGHHIYSSDSSFEVRGANPWIKFKSVS

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_74 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 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167301 retrocopy
retro_amel_400,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG000000054851 retrocopy
retro_eeur_580,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG00000009805 1 retrocopy
retro_nleu_74 ,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 retrocopy
retro_ptro_79,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG000000143131 retrocopy
retro_tbel_3327,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,


Copyright © RetrogeneDB 2014-2017