RetrogeneDB ID:

retro_sscr_1080

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL892520.2:40307..41057(-)
Located in intron of:ENSSSCG00000016966
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9B
Ensembl ID:ENSSSCG00000026714
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_sscr_1080
ATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGATATGGG
GATTACAGAATATGAGCCAAGAGTTATAAATCAGATGCTGGAGTTTGCCTTCCGATATGTGACCACAATTCTAGATGATG
CAAAAATTTATTCAAGTCATGCTAAGAAAGCGACTGTTGATGCAGATGATGTGAGATTGGCAATCCAGTGTCGTGCTGAC
CAATCATTTACCTCTCCTCCCCCAAGAGATTTTTTATTAGATATTGCAAGGCAAAGAAATCAAACCCCTTTGCCATTGAT
CAAGCCATATTCAGGCCCTCGATTGCCACCTGATAGATACTGTTTGACTGCTCCAAATTACAGACTTAAGTCTTTACAAA
AAAAGGCATCTACTTCTGCGGGAAGAATAACAGTTCCGCGGTTAAGTGTGGGTTCAGTTACTAGCAGACCAAGTACTCCC
ACACTTGGCACACCAACCCAACAAACCATGTCTGTTCCAGCTAAAGTAGGGACACCAGTGTCCCTCACAGGGCAAAGGTT
CACAGTACAGATGCCCACTTCACAGTCCCCAGCTGTAAAAGCATCAATTCCTGCAACATCAGCAGTTCAGAATGTTCTAA
TTAATCCATCATTAATTGGGTCCAAAAATATTCTTATTACCACTAACATGGTGTCATCACAAAATACTGCCAGTGAATCA
TCAAACGCATTGAAAAGAAAACGTGAAGAT

ORF - retro_sscr_1080 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.2 %
Parental protein coverage: 97.24 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTSILDDAKIYSSHAKKPNVDADD
MESGKMA.PK..P.DA..MAQILKDMGITEYEPRVINQMLEFAFRYVT.ILDDAKIYSSHAKK..VDADD
RetrocopyMESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADD
ParentalVRLAIQCRADQSFTSPPPRDFLLDIARQKNQTPLPLIKPYAGPRLPPDRYCLTAPNYRLKSLIKKIGPNQ
VRLAIQCRADQSFTSPPPRDFLLDIARQ.NQTPLPLIKPY.GPRLPPDRYCLTAPNYRLKSL.KK.....
RetrocopyVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLQKKASTSA
ParentalGRL-VPRLSVGAVSSRPTTPTIAAATSQTVSVPNKVAPPVSVTSQRFTVQIPPSQSTPVK-PVPATTAVQ
GR..VPRLSVG.V.SRP.TPT....T.QT.SVP.KV..PVS.T.QRFTVQ.P.SQS..VK...PAT.AVQ
RetrocopyGRITVPRLSVGSVTSRPSTPTLGTPTQQTMSVPAKVGTPVSLTGQRFTVQMPTSQSPAVKASIPATSAVQ
ParentalNVLINPSMIGPKNILITTNMVSSQNTANE-SNPLKRKHED
NVLINPS.IG.KNILITTNMVSSQNTA.E.SN.LKRK.ED
RetrocopyNVLINPSLIGSKNILITTNMVSSQNTASESSNALKRKRED

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
SRP014902_placenta 0 .00 RPM 6 .77 RPM
SRP014902_testis 0 .28 RPM 14 .00 RPM
SRP018288_heart 0 .03 RPM 25 .62 RPM
SRP018288_kidney 0 .30 RPM 18 .13 RPM
SRP018288_liver 0 .32 RPM 7 .68 RPM
SRP018288_lung 0 .00 RPM 16 .90 RPM
SRP018856_adipose 0 .00 RPM 11 .73 RPM
SRP035408_brain 0 .00 RPM 14 .42 RPM
SRP035408_liver 0 .00 RPM 5 .67 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_sscr_1080 retrocopy
EST ID Start End Identity Match Mis-match Score
EW321553 51342595 51342927 100 332 0 332

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_1080 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1080 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 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 ENSRNOG000000024531 retrocopy
retro_rnor_1492,
Sus scrofa ENSSSCG00000026714 2 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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