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This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
RFX3 (Regulatory Factor X3) is a Protein Coding gene. Diseases associated with RFX3 include Cellular Ependymoma and Visceral Heterotaxy. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is RFX2.
GeneHancer (GH) Identifier | GH Type | GH Score |
GH Sources | Gene Association Score | Total Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites |
Gene Targets |
---|---|---|---|---|---|---|---|---|---|---|
GH09J003523 | Promoter/Enhancer | 2.4 | EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER | 600.7 | 0.0 | -25 | 6.7 | SP1 HNRNPL CREB1 ZNF629 PRDM10 REST RFX1 SOX13 NFKBIZ POLR2A | RFX3 RFX3-AS1 piR-48209-683 GLIS3 | |
GH09J003473 | Promoter/Enhancer | 0.7 | EPDnew ENCODE | 600.2 | +52.9 | 52918 | 0.2 | SPI1 MAX CTCF | piR-37472-010 RFX3 lnc-KCNV2-7 PUM3 | |
GH09J002630 | Enhancer | 0.6 | Ensembl ENCODE | 11.9 | +896.3 | 896328 | 0.8 | ZNF157 ZNF316 MAFF MAFK MAFG EMSY | RFX3 PUM3 piR-54979 VLDLR VLDLR-AS1 KCNV2 | |
GH09J004499 | Enhancer | 1 | Ensembl ENCODE dbSUPER | 6.1 | -975.2 | -975205 | 3.8 | REST SP1 FOXA2 ATF3 YY1 GABPA ZBTB33 JUND NFIC NFIB | RFX3 SLC1A1 piR-57176-628 PLPP6 | |
GH09J003507 | Enhancer | 1.3 | FANTOM5 ENCODE dbSUPER | 2.4 | +17.7 | 17680 | 3.1 | PRDM10 RFX1 PRDM1 RELA ZSCAN4 ZNF24 IKZF2 BRD9 ZNF501 TRIM22 | RFX3 lnc-KCNV2-9 lnc-KCNV2-8 PUM3 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000976 | transcription regulatory region sequence-specific DNA binding | IDA | 20148032 |
GO:0000978 | RNA polymerase II proximal promoter sequence-specific DNA binding | IBA | 21873635 |
GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | TAS,ISM | 19274049 |
GO:0003677 | DNA binding | TAS | 8600444 |
GO:0003700 | DNA-binding transcription factor activity | NAS,IBA | 21873635 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000790 | nuclear chromatin | IDA,ISA | -- |
GO:0005576 | extracellular region | IEA | -- |
GO:0005634 | nucleus | TAS,IC | 12411430 |
GO:0005667 | transcription factor complex | IC | 20413507 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0006351 | transcription, DNA-templated | IEA | -- |
GO:0006355 | regulation of transcription, DNA-templated | ISS | -- |
GO:0006357 | regulation of transcription by RNA polymerase II | IBA | 21873635 |
GO:0007275 | multicellular organism development | IEA | -- |
GO:0007368 | determination of left/right symmetry | IEA | -- |
This gene was present in the common ancestor of animals.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Cow (Bos Taurus) |
Mammalia | RFX3 31 |
|
OneToOne | |
LOC538070 30 |
|
||||
Chimpanzee (Pan troglodytes) |
Mammalia | RFX3 30 |
|
||
Oppossum (Monodelphis domestica) |
Mammalia | RFX3 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | RFX3 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | RFX3 30 31 |
|
OneToOne | |
Mouse (Mus musculus) |
Mammalia | Rfx3 30 17 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | RFX3 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | RFX3 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | rfx3 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | rfx3 30 31 |
|
OneToOne | |
African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP003943 30 |
|
||
Fruit Fly (Drosophila melanogaster) |
Insecta | Rfx 30 31 32 |
|
OneToMany | |
Worm (Caenorhabditis elegans) |
Secernentea | daf-19 30 |
|
||
Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
OneToMany | |
Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.4580 30 |
|
SNP ID | Clinical significance and condition | Chr 09 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
768277 | Benign: not provided | 3,257,053(-) | A/G | SYNONYMOUS_VARIANT | |
776762 | Likely Benign: not provided | 3,248,035(-) | G/A | SYNONYMOUS_VARIANT | |
778032 | Benign: not provided | 3,228,838(-) | G/A | INTRON_VARIANT | |
778377 | Benign: not provided | 3,257,122(-) | C/T | SYNONYMOUS_VARIANT | |
788672 | Benign: not provided | 3,271,018(-) | G/A | MISSENSE_VARIANT |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
esv1255308 | CNV | insertion | 17803354 |
esv2477708 | CNV | deletion | 19546169 |
esv2659402 | CNV | deletion | 23128226 |
esv2762782 | CNV | loss | 21179565 |
esv3331489 | CNV | insertion | 20981092 |
esv3544440 | CNV | deletion | 23714750 |
esv3619307 | CNV | loss | 21293372 |
esv3619310 | CNV | loss | 21293372 |
esv3619312 | CNV | loss | 21293372 |
nsv1017474 | CNV | gain | 25217958 |
nsv1077086 | CNV | deletion | 25765185 |
nsv1136013 | CNV | deletion | 24896259 |
nsv1148671 | CNV | deletion | 26484159 |
nsv415859 | CNV | insertion | 16902084 |
nsv416089 | CNV | insertion | 16902084 |
nsv466091 | CNV | loss | 19166990 |
nsv522711 | CNV | gain | 19592680 |
nsv613145 | CNV | loss | 21841781 |
nsv613146 | CNV | loss | 21841781 |
nsv613147 | CNV | loss | 21841781 |
nsv950831 | CNV | duplication | 24416366 |
nsv956145 | CNV | deletion | 24416366 |
nsv972292 | CNV | duplication | 23825009 |
Disorder | Aliases | PubMed IDs |
---|---|---|
cellular ependymoma |
|
|
visceral heterotaxy |
|
|
primary ciliary dyskinesia |
|
|