RetrogeneDB ID:

retro_rnor_1492

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:49827039..49827789(+)
Located in intron of:ENSRNOG00000039848
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Taf9b
Ensembl ID:ENSRNOG00000002453
Aliases:None
Description:Transcription initiation factor TFIID subunit 9B [Source:UniProtKB/Swiss-Prot;Acc:Q62880]


Retrocopy-Parental alignment summary:






>retro_rnor_1492
ATGGAGTCTGGCAAGATGGCGTCTCCCAAGAGCATGCCGAAAGACGCACAGATGATGGCACAAATCCTGAAGGATATGGG
GATTACAGAGTATGAGCCAAGAGTTATAAATCAGATGCTGGAGTTTGCCTTCCGATATGTGACCACAATTCTAGATGATG
CTAAAATTTATTCAAGCCATGCTAAGAAACCTACTGTTGATGCAGATGATGTCCGATTGGCAATCCAGTGCCGTGCTGAC
CAGTCTTTCACTTCTCCTCCCCCGAGAGATTTTTTATTAGATATTGCAAGGCAAAGAAATCAAACCCCTTTGCCATTGAT
CAAGCCATATTCAGGTCCTAGATTGCCACCTGATAGATACTGCTTAACTGCTCCAAACTATAGGCTTAAGTCTTTACAAA
AAAAGGCACCTACTCCTGCAGGAAGAATAACGGTTCCAAGGTTAAGTGTTGGTTCAGTTTCTAGTAGACCTAGTACTCCC
ACACTAGGCACACCAACTCCACAAGCCATGTCTGTGTCAACTAAAGTAGGCACTCCAATGTCCCTCACAGGGCAGAGGTT
TACAGTACAGATGCCTGCTTCTCAGTCCCCTGCTGTAAAAGCTTCCATTCCTGCAACACCAGCAGTTCAGAATGTTCTTA
TTAATCCATCATTAATTGGGTCCAAAAACATTCTTATTACTACTAATATGGTGTCACAAAATACAGCCAATGAGTCGGCA
AACGCACTCAAAAGAAAACGTGAAGAAGAA

ORF - retro_rnor_1492 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.4 %
Parental protein coverage: 94.96 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEPSKMAPLKNAPRDALVMAQILKDMGITDYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD
ME..KMA..K..P.DA..MAQILKDMGIT.YEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD
RetrocopyMESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPTVDADD
ParentalVRLAIQCRADQSFTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLVKKGPN-Q
VRLAIQCRADQSFTSPPPRDFLLDIARQ.NQTPLPLIKPY.GPRLPPDRYCLTAPNYRLKSL.KK.P...
RetrocopyVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLQKKAPTPA
ParentalGRL-VPRLSVGAVSSRPTTPTVA--PPQAVSVPNKVATPVSVTSQRFAVQIPTSQSTPAKPA-PAATSVQ
GR..VPRLSVG.VSSRP.TPT.....PQA.SV..KV.TP.S.T.QRF.VQ.P.SQS...K...PA...VQ
RetrocopyGRITVPRLSVGSVSSRPSTPTLGTPTPQAMSVSTKVGTPMSLTGQRFTVQMPASQSPAVKASIPATPAVQ
ParentalNVLINPSMIGSKNILITTNMVSSQSTATDSNPLKRKHDDD
NVLINPS.IGSKNILITTNMVS........N.LKRK....
RetrocopyNVLINPSLIGSKNILITTNMVSQNTANESANALKRKREEE

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
SRP017611_brain 42 .13 RPM 44 .79 RPM
SRP017611_kidney 27 .22 RPM 18 .35 RPM
SRP017611_liver 12 .17 RPM 3 .56 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_rnor_1492 retrocopy
EST ID Start End Identity Match Mis-match Score
AW140683 49827259 49827411 97.4 148 4 144

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1492 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1492 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2145
Pongo abelii retro_pabe_2748
Mus musculus retro_mmus_161
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 ENSPPYG000000204974 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 ENSRNOG00000002453 1 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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