RetrogeneDB ID:

retro_ecab_303

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:14:92709751..92710492(+)
Located in intron of:ENSECAG00000015185
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9B
Ensembl ID:ENSECAG00000010189
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_ecab_303
ATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAGATCCTGAAGGATATGGG
CATTACAGAGTACGAGCCAAGAGTTATAAATCAGATGTTGGAGTTTGCCTTCCGATATGTGACCACAATTCTAGATGATG
CAAAAATTTATTCAAGCCATGCTAAGAAAGCTACTGTTGATGCCGATGATGTGCGATTGGCAATCCAGTGTCGTGCTGAC
CAGTCTTTTACCTCTCCTCCCCCAAGAGATTTTTTATTGGATATTGCACGGCAAAGAAATCAAACCCCTTTGCCATTGAT
CAAGCCCTATTCGGGCCCTAGGTTGCCACCTGATAGATATTGTTTGACTGCTCCAAATTATAGACTTAAGTCTTTACAGA
AAAAGGCATCTACTTCTGCGGGAAGAATAACAGTTCCGCGGTTAAGTGTTGGTTCAGTTACTAGCAGACCAAGTACTCCC
ACTCTTGGCACACCAACCCCACAGACCGTGTCTGTTTCAACCAAGGTAGGGACTCCAGTATCCCTCACAGGGCAGAGGTT
TACGGTGCAGATGCCCACCTCGCAGTCCCCAGCTGTAAAAGCGTCCATTCCTGCAACATCAGCAGTTCAGAATGTTCTGA
TTAATCCGTCATTAATCGGGTCCAAAAACATTCTTATTACCACTAACATGGTGTCATCACAGAATACTGCCAGTGAATCA
TCAAATACATCGAAAAGAAAG

ORF - retro_ecab_303 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.38 %
Parental protein coverage: 94.51 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDADD
MESGKMA.PK..P.DA..MAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKK..VDADD
RetrocopyMESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADD
ParentalVRLAIQCRADQSFTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLVKKGA-NQ
VRLAIQCRADQSFTSPPPRDFLLDIARQ.NQTPLPLIKPY.GPRLPPDRYCLTAPNYRLKSL.KK.....
RetrocopyVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLQKKASTSA
ParentalGRL-VPRLSVGAVSSRPTTPTVA--TPQTVSVPNKVAPPASVTSQRFTVQIPPSQSTPVK-PVPATTAVQ
GR..VPRLSVG.V.SRP.TPT....TPQTVSV..KV..P.S.T.QRFTVQ.P.SQS..VK...PAT.AVQ
RetrocopyGRITVPRLSVGSVTSRPSTPTLGTPTPQTVSVSTKVGTPVSLTGQRFTVQMPTSQSPAVKASIPATSAVQ
ParentalNVLINPSMIGSKNILITTNMVSSQNMANE-SNPLKRK
NVLINPS.IGSKNILITTNMVSSQN.A.E.SN..KRK
RetrocopyNVLINPSLIGSKNILITTNMVSSQNTASESSNTSKRK

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
SRP021940_articular_cartilage 9 .68 RPM 1 .89 RPM
SRP021940_cerebellum 27 .37 RPM 2 .29 RPM
SRP021940_embryo 36 .03 RPM 5 .04 RPM
SRP021940_placental_villous 22 .03 RPM 1 .49 RPM
SRP021940_synovial_membrane 15 .98 RPM 2 .47 RPM
SRP021940_testis 212 .74 RPM 0 .77 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_303 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_303 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_303 has 0 orthologous retrocopies within eutheria group .

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 ENSECAG00000010189 1 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 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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