Nxf3 (nuclear RNA export factor 3) - Rat Genome Database

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Gene: Nxf3 (nuclear RNA export factor 3) Rattus norvegicus
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Symbol: Nxf3
Name: nuclear RNA export factor 3
RGD ID: 1564923
Description: Predicted to enable mRNA binding activity. Predicted to be involved in poly(A)+ mRNA export from nucleus. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of nuclear RNA export factor complex. Predicted to be active in nucleus. Orthologous to human NXF3 (nuclear RNA export factor 3); PARTICIPATES IN CRM1 export pathway; influenza A pathway; mRNA decay pathway; INTERACTS WITH bisphenol A; 2,2',5,5'-tetrachlorobiphenyl (ortholog); all-trans-retinoic acid (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC302591; RGD1564923; similar to nuclear RNA export factor 2
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X103,817,508 - 103,842,038 (-)NCBIGRCr8
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX99,025,901 - 99,039,261 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX101,161,543 - 101,173,875 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X104,672,156 - 104,684,488 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X102,224,004 - 102,236,334 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X106,562,957 - 106,587,487 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX106,563,984 - 106,576,314 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X106,534,942 - 106,559,308 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X123,329,678 - 123,342,473 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX100,106,880 - 100,119,210 (+)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Postage for the messenger: designating routes for nuclear mRNA export. Natalizio BJ and Wente SR, Trends Cell Biol. 2013 Aug;23(8):365-73. doi: 10.1016/j.tcb.2013.03.006. Epub 2013 Apr 11.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11545741   PMID:15820316  


Genomics

Comparative Map Data
Nxf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X103,817,508 - 103,842,038 (-)NCBIGRCr8
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX99,025,901 - 99,039,261 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX101,161,543 - 101,173,875 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X104,672,156 - 104,684,488 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X102,224,004 - 102,236,334 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X106,562,957 - 106,587,487 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX106,563,984 - 106,576,314 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X106,534,942 - 106,559,308 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X123,329,678 - 123,342,473 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX100,106,880 - 100,119,210 (+)NCBICelera
Cytogenetic MapXq32NCBI
NXF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X103,075,810 - 103,093,143 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX103,075,810 - 103,093,143 (-)EnsemblGRCh38hg38GRCh38
GRCh37X102,330,738 - 102,348,071 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X102,217,405 - 102,234,678 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X102,136,896 - 102,154,167NCBI
CeleraX102,769,795 - 102,787,069 (-)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX91,994,756 - 92,011,809 (-)NCBIHuRef
CHM1_1X102,223,442 - 102,240,732 (-)NCBICHM1_1
T2T-CHM13v2.0X101,520,737 - 101,538,070 (-)NCBIT2T-CHM13v2.0
Nxf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X134,972,272 - 135,040,382 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX134,972,848 - 134,986,004 (-)EnsemblGRCm39 Ensembl
GRCm38X136,071,523 - 136,139,579 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX136,072,099 - 136,085,255 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X132,606,638 - 132,619,794 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X131,418,463 - 131,431,619 (-)NCBIMGSCv36mm8
CeleraX119,387,499 - 119,400,626 (-)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX57.38NCBI
NXF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X102,681,710 - 102,700,137 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X102,685,315 - 102,703,742 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X92,300,328 - 92,317,613 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X102,679,383 - 102,696,618 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX102,679,383 - 102,696,618 (-)Ensemblpanpan1.1panPan2
NXF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_TashaX62,687,089 - 62,699,509 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X78,002,045 - 78,014,584 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX78,065,653 - 78,076,889 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X75,490,319 - 75,502,822 (+)NCBIUMICH_Zoey_3.1
UU_Cfam_GSD_1.0X76,928,146 - 76,940,682 (+)NCBIUU_Cfam_GSD_1.0
Nxf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X61,745,701 - 61,757,925 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365478,066,413 - 8,084,756 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC102164431
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X83,980,605 - 83,989,335 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X97,234,550 - 97,235,202 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NXF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X90,997,859 - 91,054,806 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX90,997,653 - 91,011,235 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606515,830,843 - 15,848,675 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Nxf3
66 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:19
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000037823
Prediction methods:Miranda, Pita, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 4 6 34 31 27 14 7 14 6 49 25 22 52 13

Sequence


Ensembl Acc Id: ENSRNOT00000037823   ⟹   ENSRNOP00000032378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX99,026,931 - 99,039,261 (-)Ensembl
Rnor_6.0 EnsemblX106,563,984 - 106,576,314 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114864   ⟹   ENSRNOP00000078706
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX99,025,901 - 99,039,234 (-)Ensembl
RefSeq Acc Id: NM_001191731   ⟹   NP_001178660
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,818,542 - 103,830,872 (-)NCBI
mRatBN7.2X99,026,931 - 99,039,261 (-)NCBI
Rnor_6.0X106,563,984 - 106,576,314 (-)NCBI
Rnor_5.0X106,534,942 - 106,559,308 (+)NCBI
CeleraX100,106,880 - 100,119,210 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773410   ⟹   XP_008771632
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,817,508 - 103,842,038 (-)NCBI
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBI
Rnor_6.0X106,562,957 - 106,587,487 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773411   ⟹   XP_008771633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,817,508 - 103,842,038 (-)NCBI
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBI
Rnor_6.0X106,562,957 - 106,587,487 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099639   ⟹   XP_038955567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,817,508 - 103,842,038 (-)NCBI
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBI
RefSeq Acc Id: XM_039099640   ⟹   XP_038955568
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,817,508 - 103,842,038 (-)NCBI
mRatBN7.2X99,025,901 - 99,050,409 (-)NCBI
RefSeq Acc Id: XM_063279929   ⟹   XP_063135999
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X103,817,508 - 103,831,894 (-)NCBI
RefSeq Acc Id: NP_001178660   ⟸   NM_001191731
- UniProtKB: F1M355 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771633   ⟸   XM_008773411
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771632   ⟸   XM_008773410
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000032378   ⟸   ENSRNOT00000037823
RefSeq Acc Id: XP_038955568   ⟸   XM_039099640
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZLL9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955567   ⟸   XM_039099639
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZLL9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000078706   ⟸   ENSRNOT00000114864
RefSeq Acc Id: XP_063135999   ⟸   XM_063279929
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZLL9 (UniProtKB/TrEMBL)
Protein Domains
NTF2   TAP-C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M355-F1-model_v2 AlphaFold F1M355 1-557 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564923 AgrOrtholog
BioCyc Gene G2FUF-1637 BioCyc
Ensembl Genes ENSRNOG00000028751 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037823 ENTREZGENE
  ENSRNOT00000037823.6 UniProtKB/TrEMBL
  ENSRNOT00000114864.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.450.50 UniProtKB/TrEMBL
  3.30.70.330 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
  DNA helicase RuvA subunit, C-terminal domain UniProtKB/TrEMBL
InterPro LRR_dom_sf UniProtKB/TrEMBL
  NTF2 UniProtKB/TrEMBL
  NTF2-like_dom UniProtKB/TrEMBL
  Nuclear_transport_factor_2_euk UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  NXF_fam UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  TAP_C UniProtKB/TrEMBL
  Tap_RNA-bd UniProtKB/TrEMBL
  UBA-like UniProtKB/TrEMBL
KEGG Report rno:302591 UniProtKB/TrEMBL
NCBI Gene 302591 ENTREZGENE
PANTHER PTHR10662 UniProtKB/TrEMBL
  PTHR10662:SF12 UniProtKB/TrEMBL
Pfam NXF_NTF2 UniProtKB/TrEMBL
  Tap-RNA_bind UniProtKB/TrEMBL
  TAP_C UniProtKB/TrEMBL
PhenoGen Nxf3 PhenoGen
PROSITE NTF2_DOMAIN UniProtKB/TrEMBL
  TAP_C UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028751 RatGTEx
SMART TAP_C UniProtKB/TrEMBL
Superfamily-SCOP SSF54427 UniProtKB/TrEMBL
  SSF54928 UniProtKB/TrEMBL
  UBA_like UniProtKB/TrEMBL
UniProt A0A8I5ZLL9 ENTREZGENE, UniProtKB/TrEMBL
  F1M355 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Nxf3  nuclear RNA export factor 3  RGD1564923_predicted  similar to nuclear RNA export factor 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564923_predicted  similar to nuclear RNA export factor 2 (predicted)  LOC302591  similar to nuclear RNA export factor 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302591  similar to nuclear RNA export factor 2      Symbol and Name status set to provisional 70820 PROVISIONAL