RetrogeneDB ID:

retro_ptro_772

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:74608469..74608993(-)
Located in intron of:None
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_772
ACCTCTTCTCCCCTAAGAGCTTTTCTGTTAGATATTGCAAGTCAAAGAAATTAAACTCCTTTGCCATTAATCAAGCCATA
TTTAGATCCTAATTCAATATCCTAACAGACATTGGTTAATCGCTTCAAACTATAGGCTTAAGTCTTTACAGAAAAAGATT
TCTACTTCTGCAGGAAGAGTAACAATTCCATGGTTAAGCATTGGTTCAGTTACTAGCAGACCAAGTAATCTTACATTAGG
TGCAACCACCCCACAAATCATGTCTGTTTTAACTAAAGTATGGACTTCAATGTCCCTCACAGTGAAAAAGGTTTACAGTA
CAGCTTTCTGCTTCACAGACTCCAGCTATAAAAGCATCAATTTCTGCAACATCATCAGTAAAGAGTGTTCCAATTAATCA
ATCATTATTTAGGTCCAAAAGCATTCTTATTACCACTAATATGGAGTCACCACAAAATATTGCCAATGGATCATCAAGTC
CATTTAAAAGGAAGCATTAAGAAGATGATAATGATAATAATGAC

ORF - retro_ptro_772 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.41 %
Parental protein coverage: 66.14 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLP-PDRYCLTAPNYRLKSLIKK-GPNQGRL-VPRLSVGA
TS.P.R.FLLDIA.Q.N.TPLPLIKPY..P....P.R..L.A.NYRLKSL.KK.....GR...P.LS.G.
RetrocopyTSSPLRAFLLDIASQRN*TPLPLIKPYLDPNSI>PNRHWLIASNYRLKSLQKKISTSAGRVTIPWLSIGS
ParentalVSSKPTTPTIA--TPQTVSVPNKVATPMSVTSQ-RFTVQIPPSQSTPVKP-VPATTAVQNVLINPSMIGP
V.S.P...T....TPQ..SV..KV.T.MS.T...RFTVQ...SQ....K....AT..V..V.IN.S....
RetrocopyVTSRPSNLTLGATTPQIMSVLTKVWTSMSLTVK>RFTVQLSASQTPAIKASISATSSVKSVPINQSLFRS
ParentalKNILITTNMVSSQNTAN-EANPLKRKH--DDDDDND
K.ILITTNM.S.QN.AN....P.KRKH..DD.D.ND
RetrocopyKSILITTNMESPQNIANGSSSPFKRKH*EDDNDNND

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






(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 .00 RPM 23 .33 RPM
SRP007412_cerebellum 0 .00 RPM 17 .53 RPM
SRP007412_heart 0 .00 RPM 17 .55 RPM
SRP007412_kidney 0 .00 RPM 21 .55 RPM
SRP007412_liver 0 .00 RPM 5 .11 RPM
SRP007412_testis 0 .00 RPM 11 .70 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_772 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_772 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_772 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_941

Parental genes homology:
Parental genes homology involve 28 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176131 retrocopy
Bos taurus ENSBTAG000000008951 retrocopy
Canis familiaris ENSCAFG000000172781 retrocopy
Callithrix jacchus ENSCJAG000000195201 retrocopy
Cavia porcellus ENSCPOG000000020982 retrocopies
Equus caballus ENSECAG000000101891 retrocopy
Erinaceus europaeus ENSEEUG000000109161 retrocopy
Felis catus ENSFCAG000000254932 retrocopies
Homo sapiens ENSG000001873251 retrocopy
Gorilla gorilla ENSGGOG000000024702 retrocopies
Macropus eugenii ENSMEUG000000096971 retrocopy
Myotis lucifugus ENSMLUG000000145811 retrocopy
Macaca mulatta ENSMMUG000000128751 retrocopy
Monodelphis domestica ENSMODG000000040771 retrocopy
Mustela putorius furoENSMPUG000000000841 retrocopy
Mus musculus ENSMUSG000000472421 retrocopy
Nomascus leucogenys ENSNLEG000000013785 retrocopies
Oryctolagus cuniculus ENSOCUG000000147171 retrocopy
Otolemur garnettii ENSOGAG000000111073 retrocopies
Pongo abelii ENSPPYG000000204974 retrocopies
Pan troglodytes ENSPTRG00000022053 4 retrocopies
Pteropus vampyrus ENSPVAG000000174081 retrocopy
Rattus norvegicus ENSRNOG000000024531 retrocopy
Sus scrofa ENSSSCG000000267142 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000019823 retrocopies
Tarsius syrichta ENSTSYG000000079681 retrocopy
Tursiops truncatus ENSTTRG000000159641 retrocopy
Vicugna pacos ENSVPAG000000012101 retrocopy



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