RetrogeneDB ID:

retro_ptro_1765

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:26168018..26168769(+)
Located in intron of:ENSPTRG00000014700
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9B
Ensembl ID:ENSPTRG00000022053
Aliases:None
Description:TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa [Source:HGNC Symbol;Acc:17306]


Retrocopy-Parental alignment summary:






>retro_ptro_1765
ATGGAATTGGGCAAGATGGCACTTCCCAAGAACGCTCCTAGGGATGCCTTGGTGATGGCACAGATCTCGAAGGATATGGG
AATCACAGACTACAAACCAAAGGTTATAAATCAAATTTTGGAATTTGCTTTCCGAAATGTGACTACAATTCTGGATGATG
CAAAAATTTATTCAAGCCATACTAAGAAACCTAATGTTGATGCAGATGATGTGAGACTGGCAATCCAGTGTCGTGCTGAT
CTTTCACCTCTCTTCCCCCAAGAGGTTTCTTACTGGATATTGCAAGGCAGAAAAATCAAACCCCTTTGCCACTGATTAAG
CCATATGCAGGACCTAGACTCCCACCTGATAGATACTGCTTAACAGCTCCAAACTATAGGCTGAAGTCCTTAATTAAAAA
GGGACCTAACCAAGGGAGGCTAGTTCTACGACTGACTGTTGGTGCTGTTAGTAGCAAACCTACCACTCCTACTATAGTGA
CCCCACAAACAGTGTCTGTCACAAATAAAGTTTCAACTCCAATGTCAGTGACAAGCCAAAGATTTAACAGTGCAGATTCC
ACCTTCTCGGTCCACACCTGTCAAACCAGTTCCTGCAACAACTGCAGTTCAAAATGTTCCAACTAATCCCTCAATGATTG
GGCCCAAAAATATTCTTATTCCCATCAACATGGTTTCGTCATAGAACACAGCCAATGAAGCAAACCCACTGAAGAGAAAA
ACATGAAGATGATGATGACAATGATACTATG

ORF - retro_ptro_1765 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.8 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDADD
ME.GKMA.PKNAPRDALVMAQI.KDMGIT.Y.P.VINQ.LEFAFR.VTTILDDAKIYSSH.KKPNVDADD
RetrocopyMELGKMALPKNAPRDALVMAQISKDMGITDYKPKVINQILEFAFRNVTTILDDAKIYSSHTKKPNVDADD
ParentalVRLAIQCRADQS-FTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLIKKGPNQ
VRLAIQCRAD.S....PP.R.FLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLIKKGPNQ
RetrocopyVRLAIQCRADLS<TSLPP-RGFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLIKKGPNQ
ParentalGRLVPRLSVGAVSSKPTTPTIATPQTVSVPNKVATPMSVTSQRF-TVQIPPSQSTPVKPVPATTAVQNVL
GRLV.RL.VGAVSSKPTTPTI.TPQTVSV.NKV.TPMSVTSQRF.TVQIPPS.STPVKPVPATTAVQNV.
RetrocopyGRLVLRLTVGAVSSKPTTPTIVTPQTVSVTNKVSTPMSVTSQRF>TVQIPPSRSTPVKPVPATTAVQNVP
ParentalINPSMIGPKNILITTNMVSSQNTANEANPLKR-KHDDDDDNDIM
.NPSMIGPKNILI..NMVSS.NTANEANPLKR.KH.DDDDND.M
RetrocopyTNPSMIGPKNILIPINMVSS*NTANEANPLKR>KHEDDDDNDTM

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .16 RPM 23 .33 RPM
SRP007412_cerebellum 0 .29 RPM 17 .53 RPM
SRP007412_heart 0 .06 RPM 17 .55 RPM
SRP007412_kidney 0 .08 RPM 21 .55 RPM
SRP007412_liver 0 .03 RPM 5 .11 RPM
SRP007412_testis 0 .21 RPM 11 .70 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1765 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1765 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1765 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2619
Gorilla gorilla retro_ggor_1833
Pongo abelii retro_pabe_2341
Macaca mulatta retro_mmul_1480
Parental genes homology:
Parental genes homology involve 28 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176131 retrocopy
retro_amel_449,
Bos taurus ENSBTAG000000008951 retrocopy
retro_btau_196,
Canis familiaris ENSCAFG000000172781 retrocopy
retro_cfam_192,
Callithrix jacchus ENSCJAG000000195201 retrocopy
retro_cjac_246,
Cavia porcellus ENSCPOG000000020982 retrocopies
retro_cpor_906, retro_cpor_967,
Equus caballus ENSECAG000000101891 retrocopy
retro_ecab_303,
Erinaceus europaeus ENSEEUG000000109161 retrocopy
retro_eeur_18,
Felis catus ENSFCAG000000254932 retrocopies
retro_fcat_1036, retro_fcat_260,
Homo sapiens ENSG000001873251 retrocopy
retro_hsap_2619,
Gorilla gorilla ENSGGOG000000024702 retrocopies
retro_ggor_1833, retro_ggor_45,
Macropus eugenii ENSMEUG000000096971 retrocopy
retro_meug_140,
Myotis lucifugus ENSMLUG000000145811 retrocopy
retro_mluc_519,
Macaca mulatta ENSMMUG000000128751 retrocopy
retro_mmul_1480,
Monodelphis domestica ENSMODG000000040771 retrocopy
retro_mdom_850,
Mustela putorius furoENSMPUG000000000841 retrocopy
retro_mputfur_63,
Mus musculus ENSMUSG000000472421 retrocopy
retro_mmus_161,
Nomascus leucogenys ENSNLEG000000013785 retrocopies
retro_nleu_1677, retro_nleu_2566, retro_nleu_637, retro_nleu_920, retro_nleu_932,
Oryctolagus cuniculus ENSOCUG000000147171 retrocopy
retro_ocun_490,
Otolemur garnettii ENSOGAG000000111073 retrocopies
retro_ogar_1128, retro_ogar_3100, retro_ogar_679,
Pongo abelii ENSPPYG000000204974 retrocopies
retro_pabe_1634, retro_pabe_2341, retro_pabe_2748, retro_pabe_941,
Pan troglodytes ENSPTRG00000022053 4 retrocopies
retro_ptro_1329, retro_ptro_1765 , retro_ptro_2145, retro_ptro_772,
Pteropus vampyrus ENSPVAG000000174081 retrocopy
retro_pvam_6,
Rattus norvegicus ENSRNOG000000024531 retrocopy
retro_rnor_1492,
Sus scrofa ENSSSCG000000267142 retrocopies
retro_sscr_1080, retro_sscr_525,
Ictidomys tridecemlineatus ENSSTOG000000019823 retrocopies
retro_itri_1640, retro_itri_411, retro_itri_763,
Tarsius syrichta ENSTSYG000000079681 retrocopy
retro_tsyr_3,
Tursiops truncatus ENSTTRG000000159641 retrocopy
retro_ttru_572,
Vicugna pacos ENSVPAG000000012101 retrocopy
retro_vpac_16,


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