NXF4 (nuclear RNA export factor 4 (pseudogene)) - Rat Genome Database

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Gene: NXF4 (nuclear RNA export factor 4 (pseudogene)) Homo sapiens
Analyze
Symbol: NXF4
Name: nuclear RNA export factor 4 (pseudogene) (Ensembl:nuclear RNA export factor 4 pseudogene)
RGD ID: 1603388
HGNC Page HGNC:8074
Description: INTERACTS WITH benzo[a]pyrene; cadmium atom; CGP 52608
Type: pseudo (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: FLJ42710; nuclear RNA export factor 4 pseudogene
Related Functional Gene: NXF1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X102,549,965 - 102,571,693 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX102,549,965 - 102,571,695 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 EnsemblX102,561,935 - 102,571,465 (+)EnsemblGRCh38hg38GRCh38
GRCh37X101,804,893 - 101,826,621 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X101,691,549 - 101,713,277 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX102,243,524 - 102,265,252 (+)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX91,470,717 - 91,492,427 (+)NCBIHuRef
CHM1_1X101,697,570 - 101,719,293 (+)NCBICHM1_1
T2T-CHM13v2.0X100,994,445 - 101,016,689 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11073998   PMID:11566096   PMID:22199357  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x1 copy number loss Global developmental delay [RCV000050386]|See cases [RCV000050386] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xq22.1(chrX:102510903-102866851)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051425]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051425]|See cases [RCV000051425] ChrX:102510903..102866851 [GRCh38]
ChrX:101773567..102121779 [GRCh37]
ChrX:101652487..102008435 [NCBI36]
ChrX:Xq22.1		 uncertain significance
GRCh38/hg38 Xq22.1-22.3(chrX:102070552-108264804)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051716]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051716]|See cases [RCV000051716] ChrX:102070552..108264804 [GRCh38]
ChrX:101325524..107508034 [GRCh37]
ChrX:101212180..107394690 [NCBI36]
ChrX:Xq22.1-22.3		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:237659-156022362)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|See cases [RCV000052327] ChrX:237659..156022362 [GRCh38]
ChrX:154326..155252027 [GRCh37]
ChrX:94326..154905221 [NCBI36]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xq13.2-27.1(chrX:73008114-140201321)x4 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052418]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052418]|See cases [RCV000052418] ChrX:73008114..140201321 [GRCh38]
ChrX:72227953..139283477 [GRCh37]
ChrX:72144678..139111143 [NCBI36]
ChrX:Xq13.2-27.1		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x1 copy number loss Global developmental delay [RCV000052986]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|Intellectual functioning disability [RCV000052988]|Global developmental delay [RCV000052989]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|See cases [RCV000052986] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:14245-155999293)x1 copy number loss Hypoplastic left heart [RCV000052982]|See cases [RCV000052982] ChrX:14245..155999293 [GRCh38]
ChrX:64245..155228958 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x3 copy number gain Global developmental delay [RCV000052984]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|See cases [RCV000052984] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:679..154896026 [NCBI36]
ChrX:Xp22.33-q28		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:304
Interacting mature miRNAs:318
Transcripts:ENST00000360035
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.


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 sensory system adipose tissue appendage
High
Medium
Low 6 1 28 13 426 20
Below cutoff 679 856 627 80 284 25 1422 464 2854 56 552 654 55 457 893

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000360035
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblX102,549,965 - 102,571,695 (+)Ensembl
RefSeq Acc Id: ENST00000416098
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblX102,561,935 - 102,571,465 (+)Ensembl
RefSeq Acc Id: NR_002216
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X102,549,965 - 102,571,693 (+)NCBI
GRCh37X101,804,893 - 101,826,621 (+)RGD
Build 36X101,691,549 - 101,713,277 (+)NCBI Archive
CeleraX102,243,524 - 102,265,252 (+)RGD
HuRefX91,470,717 - 91,492,427 (+)RGD
CHM1_1X101,697,570 - 101,719,293 (+)NCBI
T2T-CHM13v2.0X100,994,445 - 101,016,689 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC85929 (Get FASTA)   NCBI Sequence Viewer  
  EAW54735 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC NXF4 COSMIC
Ensembl Genes ENSG00000196970 Ensembl
  ENSG00000290811 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000360035 ENTREZGENE
GTEx ENSG00000196970 GTEx
  ENSG00000290811 GTEx
HGNC ID HGNC:8074 ENTREZGENE
Human Proteome Map NXF4 Human Proteome Map
NCBI Gene 55999 ENTREZGENE
OMIM 300318 OMIM
PharmGKB PA31861 PharmGKB


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-08-28 NXF4  nuclear RNA export factor 4 (pseudogene)  NXF4  nuclear RNA export factor 4 pseudogene  Symbol and/or name change 19259463 PROVISIONAL