RetrogeneDB ID:

retro_pabe_2748

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:71095617..71096364(-)
Located in intron of:ENSPPYG00000015527
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9B
Ensembl ID:ENSPPYG00000020497
Aliases:None
Description:Transcription initiation factor TFIID subunit 9B [Source:UniProtKB/Swiss-Prot;Acc:Q5R7P7]


Retrocopy-Parental alignment summary:






>retro_pabe_2748
GATATCATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGA
TATGGGGATTACAGAATATGAGCCAAGAGTTATAAATCAGATGTTGGAGTTTGCCTTCCGATATGTGACCACAATTCTAG
ATGATGCAAAAATTTATTCAAGCCATGCTAAGAAAGCTACTGTTGATGCAGATGATGTGCGATTGGCAATCCAGTGCCGC
GCTGATCAGTCTTTTACCTCTCCTCCCCCAAGAGATTTTTTATTAGATATTGCAAGGCAAAGAAATCAAACCCCTTTGCC
ATTGATCAAGCCATATTCAGGTCCTAGGTTGCCACCTGATAGATATTGCTTAACAGCTCCAAACTATAGGCTGAAATCTT
TACAGAAAAAGGCATCAACTTCTGCGGGAAGAATAACAGTCCCGCGGTTAAGTGTTGGTTCAGTTACTAGCAGACCAAGT
ACTCCCACACTAGGCACACCAACCCCACAGACCATGTCTGTTTCAACTAAAGTAGGGACTCCCATGTCCCTCACAGGTCA
AAGGTTTACAGTACAGATGCCTGCTTCTCAGTCTCCAGCTGTAAAAGCTTCAATTCCTGCAACCTCAGCAGTTCAGAATG
TTTTGATTAATCCATCATTAATCGGGTCCAAAAACATTCTTATTACCACTAATATGGTGTCATCACAAAATACTGCCAAT
GAATCATCAAATGCATTGAAAAGAAAA

ORF - retro_pabe_2748 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.53 %
Parental protein coverage: 87.73 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalDNMESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDA
D.MESGKMA.PK..P.DA..MAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKK..VDA
RetrocopyDIMESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDA
ParentalDDVRLAIQCRADQSFTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLIKK-GP
DDVRLAIQCRADQSFTSPPPRDFLLDIARQ.NQTPLPLIKPY.GPRLPPDRYCLTAPNYRLKSL.KK...
RetrocopyDDVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLQKKAST
ParentalNQGRL-VPRLSVGAVSSKPTTPTIA--TPQTVSVPNKVATPMSVTSQRFTVQIPPSQSTPVK-PVPATTA
..GR..VPRLSVG.V.S.P.TPT....TPQT.SV..KV.TPMS.T.QRFTVQ.P.SQS..VK...PAT.A
RetrocopySAGRITVPRLSVGSVTSRPSTPTLGTPTPQTMSVSTKVGTPMSLTGQRFTVQMPASQSPAVKASIPATSA
ParentalVQNVLINPSMIGPKNILITTNMVSSQNTANE-ANPLKRK
VQNVLINPS.IG.KNILITTNMVSSQNTANE..N.LKRK
RetrocopyVQNVLINPSLIGSKNILITTNMVSSQNTANESSNALKRK

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 19 .30 RPM 9 .07 RPM
SRP007412_cerebellum 16 .90 RPM 15 .69 RPM
SRP007412_heart 9 .45 RPM 7 .19 RPM
SRP007412_kidney 11 .50 RPM 11 .07 RPM
SRP007412_liver 15 .12 RPM 6 .24 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2748 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2748 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2748 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2145
Mus musculus retro_mmus_161
Rattus norvegicus retro_rnor_1492
Oryctolagus cuniculus retro_ocun_490
Bos taurus retro_btau_196
Canis familiaris retro_cfam_192
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 ENSPPYG00000020497 4 retrocopies
retro_pabe_1634, retro_pabe_2341, retro_pabe_2748 , retro_pabe_941,
Pan troglodytes ENSPTRG000000220534 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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