Nfxl1 (nuclear transcription factor, X-box binding-like 1) - Rat Genome Database

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Gene: Nfxl1 (nuclear transcription factor, X-box binding-like 1) Rattus norvegicus
Analyze
Symbol: Nfxl1
Name: nuclear transcription factor, X-box binding-like 1
RGD ID: 1359201
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in membrane. Predicted to be active in nucleus. Orthologous to human NFXL1 (nuclear transcription factor, X-box binding like 1); INTERACTS WITH (+)-schisandrin B; bisphenol A; N-methyl-4-phenylpyridinium.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC289595; NF-X1-type zinc finger protein NFXL1; RGD1359201; similar to CG15011-PA; similar to nuclear transcription factor, X-box binding-like 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,980,058 - 36,021,478 (+)NCBIGRCr8
mRatBN7.21435,626,086 - 35,667,505 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,626,066 - 35,667,498 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,991,372 - 36,032,388 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,296,126 - 37,337,142 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,784,495 - 35,825,508 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01438,192,462 - 38,233,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,192,446 - 38,233,852 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,003,494 - 38,044,774 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,054,861 - 38,095,844 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11438,082,031 - 38,099,193 (+)NCBI
Celera1434,878,053 - 34,918,828 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
nucleus  (IBA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:19946888  


Genomics

Comparative Map Data
Nfxl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,980,058 - 36,021,478 (+)NCBIGRCr8
mRatBN7.21435,626,086 - 35,667,505 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,626,066 - 35,667,498 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,991,372 - 36,032,388 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,296,126 - 37,337,142 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,784,495 - 35,825,508 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01438,192,462 - 38,233,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,192,446 - 38,233,852 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,003,494 - 38,044,774 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,054,861 - 38,095,844 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11438,082,031 - 38,099,193 (+)NCBI
Celera1434,878,053 - 34,918,828 (+)NCBICelera
Cytogenetic Map14p11NCBI
NFXL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38447,847,233 - 47,914,667 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl447,847,233 - 47,914,667 (-)EnsemblGRCh38hg38GRCh38
GRCh37447,849,250 - 47,916,684 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36447,544,014 - 47,611,390 (-)NCBINCBI36Build 36hg18NCBI36
Celera448,298,135 - 48,365,585 (-)NCBICelera
Cytogenetic Map4p12NCBI
HuRef447,168,755 - 47,236,269 (-)NCBIHuRef
CHM1_1447,848,204 - 47,915,792 (-)NCBICHM1_1
T2T-CHM13v2.0447,814,565 - 47,881,968 (-)NCBIT2T-CHM13v2.0
Nfxl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39572,670,647 - 72,717,078 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl572,670,644 - 72,717,027 (-)EnsemblGRCm39 Ensembl
GRCm38572,513,304 - 72,559,735 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl572,513,301 - 72,559,684 (-)EnsemblGRCm38mm10GRCm38
MGSCv37572,904,543 - 72,950,884 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36572,835,570 - 72,838,148 (-)NCBIMGSCv36mm8
Celera569,767,855 - 69,808,087 (-)NCBICelera
Cytogenetic Map5C3.2NCBI
cM Map538.44NCBI
Nfxl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955443668,031 - 713,481 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955443665,235 - 714,627 (+)NCBIChiLan1.0ChiLan1.0
NFXL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2379,944,440 - 80,013,688 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1480,207,453 - 80,274,861 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0474,234,523 - 74,301,966 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1484,966,959 - 85,034,154 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl484,967,076 - 85,034,154 (+)Ensemblpanpan1.1panPan2
NFXL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11343,743,271 - 43,814,899 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1343,744,181 - 43,814,520 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1343,695,854 - 43,767,093 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01344,342,939 - 44,414,377 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1344,342,946 - 44,414,375 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11344,020,805 - 44,091,824 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01343,552,949 - 43,623,828 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01344,435,784 - 44,507,011 (-)NCBIUU_Cfam_GSD_1.0
Nfxl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528532,235,545 - 32,289,403 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648214,009,724 - 14,062,207 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648214,008,825 - 14,062,654 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFXL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl837,812,911 - 37,875,540 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1837,812,378 - 37,875,582 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2839,788,607 - 39,845,909 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NFXL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1272,333,158 - 2,401,008 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl272,333,809 - 2,400,084 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604748,351,769 - 48,419,293 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nfxl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476119,029,434 - 19,084,307 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476119,029,537 - 19,084,156 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nfxl1
179 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:382
Count of miRNA genes:229
Interacting mature miRNAs:283
Transcripts:ENSRNOT00000003131
Prediction methods:Microtar, Miranda, Targetscan
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat

Markers in Region
RH141380  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21435,627,844 - 35,628,044 (+)MAPPERmRatBN7.2
Rnor_6.01438,194,221 - 38,194,420NCBIRnor6.0
Rnor_5.01438,005,239 - 38,005,438UniSTSRnor5.0
RGSC_v3.41438,056,212 - 38,056,411UniSTSRGSC3.4
Celera1434,879,812 - 34,880,011UniSTS
Cytogenetic Map14p11UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 18 25 15 19 15 74 22 37 10
Low 3 25 32 26 26 8 11 13 4 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077080   ⟹   ENSRNOP00000074217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,626,086 - 35,667,498 (+)Ensembl
Rnor_6.0 Ensembl1438,192,870 - 38,233,852 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090242   ⟹   ENSRNOP00000075378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,626,066 - 35,667,498 (+)Ensembl
Rnor_6.0 Ensembl1438,192,446 - 38,233,534 (+)Ensembl
RefSeq Acc Id: NM_001170438   ⟹   NP_001163909
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,980,083 - 36,021,478 (+)NCBI
mRatBN7.21435,626,086 - 35,667,498 (+)NCBI
Rnor_6.01438,192,462 - 38,233,852 (+)NCBI
Rnor_5.01438,003,494 - 38,044,774 (+)NCBI
RGSC_v3.41438,054,861 - 38,095,844 (+)RGD
Celera1434,878,053 - 34,918,828 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091704   ⟹   XP_038947632
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,980,139 - 36,021,478 (+)NCBI
mRatBN7.21435,626,139 - 35,667,505 (+)NCBI
RefSeq Acc Id: XM_039091705   ⟹   XP_038947633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,987,691 - 36,021,478 (+)NCBI
mRatBN7.21435,633,694 - 35,667,505 (+)NCBI
RefSeq Acc Id: XM_063272918   ⟹   XP_063128988
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,980,058 - 36,021,478 (+)NCBI
RefSeq Acc Id: XM_063272919   ⟹   XP_063128989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,980,137 - 36,021,478 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001163909   ⟸   NM_001170438
- UniProtKB: F1LNF3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074217   ⟸   ENSRNOT00000077080
RefSeq Acc Id: ENSRNOP00000075378   ⟸   ENSRNOT00000090242
RefSeq Acc Id: XP_038947632   ⟸   XM_039091704
- Peptide Label: isoform X2
- UniProtKB: F1LNF3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038947633   ⟸   XM_039091705
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063128988   ⟸   XM_063272918
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAF4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063128989   ⟸   XM_063272919
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAF4 (UniProtKB/TrEMBL)
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LNF3-F1-model_v2 AlphaFold F1LNF3 1-919 view protein structure

Transcriptome

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

Promoters
RGD ID:13699308
Promoter ID:EPDNEW_R9825
Type:initiation region
Name:Nfxl1_1
Description:nuclear transcription factor, X-box binding-like 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01438,192,541 - 38,192,601EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359201 AgrOrtholog
BioCyc Gene G2FUF-15850 BioCyc
Ensembl Genes ENSRNOG00000058588 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077080.2 UniProtKB/TrEMBL
  ENSRNOT00000090242 ENTREZGENE
  ENSRNOT00000090242.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7317845 IMAGE-MGC_LOAD
InterPro NFX1_fam UniProtKB/TrEMBL
  Znf_NFX1 UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
MGC_CLONE MGC:105619 IMAGE-MGC_LOAD
NCBI Gene 289595 ENTREZGENE
PANTHER NF-X1-TYPE ZINC FINGER PROTEIN NFXL1 UniProtKB/TrEMBL
  PTHR12360 UniProtKB/TrEMBL
Pfam zf-NF-X1 UniProtKB/TrEMBL
PhenoGen Nfxl1 PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058588 RatGTEx
SMART ZnF_NFX UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
UniProt A0A0G2KAF4 ENTREZGENE, UniProtKB/TrEMBL
  F1LNF3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Nfxl1  nuclear transcription factor, X-box binding-like 1  RGD1359201  similar to nuclear transcription factor, X-box binding-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 RGD1359201  similar to nuclear transcription factor, X-box binding-like 1      Symbol and Name updated 1299863 APPROVED
2005-07-29 LOC289595  similar to CG15011-PA      Symbol and Name status set to provisional 70820 PROVISIONAL