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Aliases for RNU4ATAC Gene

Subcategory (RNA class) for RNU4ATAC Gene

snRNA

Quality Score for this RNA gene is

3

Aliases for RNU4ATAC Gene

  • RNA, U4atac Small Nuclear (U12-Dependent Splicing) 2 3 5
  • RNU4ATAC1 3
  • U4atac 3
  • MOPD1 3
  • RFMN 3
  • TALS 3

External Ids for RNU4ATAC Gene

ORGUL Members for RNU4ATAC Gene

Previous GeneCards Identifiers for RNU4ATAC Gene

  • GC02U901429
  • GC02P122289
  • GC02P114611
  • GC02P122290
  • GC02P122294
  • GC02P122297

Summaries for RNU4ATAC Gene

Entrez Gene Summary for RNU4ATAC Gene

  • The small nuclear RNA (snRNA) encoded by this gene is part of the U12-dependent minor spliceosome complex. In addition to the encoded RNA, this ribonucleoprotein complex consists of U11, U12, U5, and U6atac snRNAs. The U12-dependent spliceosome acts on approximately 700 specific introns in the human genome. Defects in this gene are a cause of microcephalic osteodysplastic primordial dwarfism type 1 (MOPD). [provided by RefSeq, Jul 2011]

GeneCards Summary for RNU4ATAC Gene

RNU4ATAC (RNA, U4atac Small Nuclear (U12-Dependent Splicing)) is an RNA Gene, and is affiliated with the snRNA class. Diseases associated with RNU4ATAC include Microcephalic Osteodysplastic Primordial Dwarfism, Type I and Roifman Syndrome.

fRNAdb sequence ontologies for RNU4ATAC Gene

  • U4atac minor spliceosomal RNA: U4atac is an essential component of the minor U12-type spliceosome complex which is required for removal of the rarer class of eukaryotic introns (AT-AC, U12-type) [1]. U4atac snRNA is proposed to form a base-paired complex with another spliceosomal RNA U6atac via two stem loop regions. These interacting stem loops have been shown to be required for in vivo splicing [2]. U4atac also contains an 3' Sm protein binding site which has been shown to be essential for splicing activity [2]. U4atac is the functional analog of U4 (Rfam:RF00015) in the major U2-type spliceosomal complex [2]. The drosophila U4atac snRNA has an additional predicted 3' stem loop terminal to the Sm binding site [3] which is not included in this model.

Additional gene information for RNU4ATAC Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for RNU4ATAC Gene

Genomics for RNU4ATAC Gene

GeneHancer (GH) Regulatory Elements for RNU4ATAC Gene

Promoters and enhancers for RNU4ATAC Gene
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
GH02I121524 Promoter/Enhancer 2 Ensembl ENCODE dbSUPER 550.8 -1.8 -1841 9.2 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 GC02P121532 RNU4ATAC ENSG00000265451 NIFK TSN LINC01823 CLASP1 GC02M121346
GH02I121721 Enhancer 1.2 FANTOM5 Ensembl ENCODE 13.1 +191.7 191694 2.1 MEIS2 ATF1 PKNOX1 ARNT JUN CEBPG RFX5 FOSL1 FOSL2 FOS CLASP1 RNU4ATAC NPM1P32 NIFK NIFK-AS1
GH02I121564 Enhancer 1.1 Ensembl ENCODE 11.8 +35.7 35692 5 PKNOX1 FOXA2 ARID4B DMAP1 ZNF48 TCF12 ZNF280A SLC30A9 ZNF766 ATF7 RNU4ATAC CLASP1 LINC01823 GC02P121556 ENSG00000222467
GH02I121718 Enhancer 0.8 Ensembl ENCODE 13.1 +188.0 188021 0.6 CTCF KLF11 RXRA TEAD1 TRIM22 REST EBF1 RAD21 ZNF121 ZNF143 CLASP1 RNU4ATAC NPM1P32 NIFK NIFK-AS1
GH02I121569 Enhancer 0.3 ENCODE 11.8 +39.0 38978 1.4 ZNF341 RNU4ATAC CLASP1 LINC01823 GC02P121556 ENSG00000222467
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNU4ATAC on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNU4ATAC gene promoter:

Genomic Locations for RNU4ATAC Gene

Genomic Locations for RNU4ATAC Gene
chr2:121,530,880-121,531,009
(GRCh38/hg38)
Size:
130 bases
Orientation:
Plus strand
chr2:122,288,456-122,288,585
(GRCh37/hg19)

Genomic View for RNU4ATAC Gene

Genes around RNU4ATAC on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNU4ATAC Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNU4ATAC Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNU4ATAC Gene

Proteins for RNU4ATAC Gene

Post-translational modifications for RNU4ATAC Gene

No Post-translational modifications

No data available for DME Specific Peptides for RNU4ATAC Gene

Domains & Families for RNU4ATAC Gene

Gene Families for RNU4ATAC Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNU4ATAC: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for RNU4ATAC Gene

Function for RNU4ATAC Gene

Human Phenotype Ontology for RNU4ATAC Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RNU4ATAC Gene

Localization for RNU4ATAC Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNU4ATAC gene
Compartment Confidence
nucleus 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for RNU4ATAC Gene

Pathways & Interactions for RNU4ATAC Gene

SuperPathways for RNU4ATAC Gene

No Data Available

Interacting Proteins for RNU4ATAC Gene

Gene Ontology (GO) - Biological Process for RNU4ATAC Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RNU4ATAC Gene

Drugs & Compounds for RNU4ATAC Gene

No Compound Related Data Available

Transcripts for RNU4ATAC Gene

mRNA/cDNA for RNU4ATAC Gene

(2) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RNU4ATAC Gene

RNA, U4atac small nuclear (U12-dependent splicing):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNU4ATAC Gene

No ASD Table

Relevant External Links for RNU4ATAC Gene

GeneLoc Exon Structure for
RNU4ATAC
ECgene alternative splicing isoforms for
RNU4ATAC

Expression for RNU4ATAC Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNU4ATAC Gene

NURSA nuclear receptor signaling pathways regulating expression of RNU4ATAC Gene:

RNU4ATAC

SOURCE GeneReport for Unigene cluster for RNU4ATAC Gene:

Hs.689638

Phenotype-based relationships between genes and organs from Gene ORGANizer for RNU4ATAC Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • pituitary gland
  • scalp
  • sinus
  • skull
  • tongue
  • tooth
  • vocal cord
Thorax:
  • aorta
  • breast
  • bronchus
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
  • liver
  • spleen
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • placenta
  • prostate
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • lymph node
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with RNU4ATAC: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for RNU4ATAC Gene

Orthologs for RNU4ATAC Gene

Evolution for RNU4ATAC Gene

ENSEMBL:
Gene Tree for RNU4ATAC (if available)
TreeFam:
Gene Tree for RNU4ATAC (if available)

No data available for Orthologs for RNU4ATAC Gene

Paralogs for RNU4ATAC Gene

No data available for Paralogs for RNU4ATAC Gene

Variants for RNU4ATAC Gene

Sequence variations from dbSNP and Humsavar for RNU4ATAC Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs180755563 pathogenic, Osteodysplastic primordial dwarfism, type 1 121,530,932(+) C/A/G/T non_coding_transcript_variant
rs181195449 pathogenic, Osteodysplastic primordial dwarfism, type 1 121,530,929(+) G/A/C non_coding_transcript_variant
rs188343279 pathogenic, Osteodysplastic primordial dwarfism, type 1, Roifman syndrome 121,530,930(+) G/A non_coding_transcript_variant
rs370715569 pathogenic, Roifman syndrome 121,530,887(+) C/G/T non_coding_transcript_variant
rs374299350 pathogenic, Osteodysplastic primordial dwarfism, type 1 121,530,909(+) G/A/C/T non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RNU4ATAC Gene

Variant ID Type Subtype PubMed ID
nsv1011665 CNV gain 25217958
nsv582798 CNV loss 21841781

Additional Variant Information for RNU4ATAC Gene

Human Gene Mutation Database (HGMD)
RNU4ATAC
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNU4ATAC

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for RNU4ATAC Gene

Disorders for RNU4ATAC Gene

MalaCards: The human disease database

(12) MalaCards diseases for RNU4ATAC Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RNU4ATAC

genes like me logo Genes that share disorders with RNU4ATAC: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RNU4ATAC Gene

Publications for RNU4ATAC Gene

  1. Refining the phenotypical and mutational spectrum of Taybi-Linder syndrome. (PMID: 27040866) Putoux A … Edery P (Clinical genetics 2016) 3 58
  2. A novel 2q14.1q14.3 deletion involving GLI2 and RNU4ATAC genes associated with partial corpus callosum agenesis and severe intrauterine growth retardation. (PMID: 27346851) Goumy C … Vago P (Birth defects research. Part A, Clinical and molecular teratology 2016) 3 58
  3. Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing. (PMID: 26522830) Merico D … Scherer SW (Nature communications 2015) 3 58
  4. Biochemical defects in minor spliceosome function in the developmental disorder MOPD I. (PMID: 24865609) Jafarifar F … Padgett RA (RNA (New York, N.Y.) 2014) 3 58
  5. Further delineation of the clinical spectrum in RNU4ATAC related microcephalic osteodysplastic primordial dwarfism type I. (PMID: 23794361) Abdel-Salam GM … Zaki MS (American journal of medical genetics. Part A 2013) 3 58

Products for RNU4ATAC Gene

Sources for RNU4ATAC Gene

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