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Aliases for SNORD42B Gene

Subcategory (RNA class) for SNORD42B Gene

snoRNA

Quality Score for this RNA gene is

12.2

Aliases for SNORD42B Gene

  • Small Nucleolar RNA, C/D Box 42B 2 3 5
  • RNA, U42B Small Nucleolar 2 3
  • U42B Small Nucleolar RNA 3
  • U42B SnoRNA 3
  • RNU42B 3
  • U42B 3

External Ids for SNORD42B Gene

ORGUL Members for SNORD42B Gene

Previous HGNC Symbols for SNORD42B Gene

  • RNU42B

Previous GeneCards Identifiers for SNORD42B Gene

  • GC17P024091
  • GC17P024096
  • GC17P024100
  • GC17P024104
  • GC17P024108
  • GC17P024112
  • GC17P024116
  • GC17P024120
  • GC17P027047
  • GC17P023256

Summaries for SNORD42B Gene

GeneCards Summary for SNORD42B Gene

SNORD42B (Small Nucleolar RNA, C/D Box 42B) is an RNA Gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORD42B Gene - the ORGUL cluster for this gene includes several descriptions:

  • nc_conserved_region: Non-coding region of sequence similarity by descent from a common ancestor.

  • C_D_box_snoRNA: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.

  • Small nucleolar RNA SNORD42: snoRNA U42 is found in intron 3 of the ribosomal protein L23a (RPL23a) gene in humans and is also present in mice. U42 is a member of the C/D class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. Although the selection of the target nucleotide requires the antisense element and the conserved box D or D' of the snoRNA, the methyltransferase activity is supposed to reside in one of the protein components [1].

View fRNAdb secondary structures for SNORD42B

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SNORD42B Gene

Genomics for SNORD42B Gene

Regulatory Elements for SNORD42B Gene

Enhancers for SNORD42B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G028863 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +144.8 144787 3.3 HDGF CREB3L1 ARNT ARID4B ZNF766 CBX5 FOS KLF13 JUNB REST DHRS13 PROCA1 FLOT2 NEK8 TLCD1 SNORD42A SNORD4B SNORD42B RAB34 RPL23A
GH17G028760 1.5 Ensembl ENCODE dbSUPER 11.8 +40.7 40722 2.2 CREB3L1 ARNT SIN3A YBX1 ETS1 ZNF766 ELK1 KLF13 ZNF592 MEF2D TRAF4 TLCD1 NEK8 SNORD4B SNORD42A ERAL1 FAM222B SNORD4A RAB34 RPL23A
GH17G028807 1.6 FANTOM5 ENCODE dbSUPER 10.7 +89.9 89890 6.8 HDGF PKNOX1 CREB3L1 ARNT AGO1 SIN3A FEZF1 DMAP1 ZNF2 YY1 TRAF4 ENSG00000264577 ENSG00000265205 NUFIP2 ENSG00000265908 ERAL1 FAM222B FLOT2 DHRS13 LOC101927018
GH17G028764 1.1 ENCODE dbSUPER 11.8 +43.4 43368 0.2 HDAC1 HDGF ATF1 NFIB WRNIP1 ARID4B BMI1 ZNF2 RAD21 RFX5 ENSG00000264577 NEK8 TLCD1 SNORD42A SNORD4B NUFIP2 ERAL1 FAM222B RPL23A SNORD42B
GH17G028911 1.2 ENCODE dbSUPER 10.6 +191.8 191776 1.3 PKNOX1 ATF1 CREB3L1 ARNT TCF12 ZNF766 GATA2 JUNB REST ZNF623 ERAL1 FAM222B SNORD42A SNORD4A RAB34 RPL23A SNORD42B DHRS13 LOC101927018
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNORD42B on UCSC Golden Path with GeneCards custom track

Promoters for SNORD42B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000092756 -250 2201 HDGF PKNOX1 FOXA2 CREB3L1 ARNT ZFP64 WRNIP1 ARID4B SIN3A DMAP1

Genomic Location for SNORD42B Gene

Chromosome:
17
Start:
28,720,550 bp from pter
End:
28,720,616 bp from pter
Size:
67 bases
Orientation:
Plus strand

Genomic View for SNORD42B Gene

Genes around SNORD42B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNORD42B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNORD42B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNORD42B Gene

ORGUL Member Location for SNORD42B Gene

ORGUL Member Location for SNORD42B gene

Proteins for SNORD42B Gene

Post-translational modifications for SNORD42B Gene

No Post-translational modifications

No data available for DME Specific Peptides for SNORD42B Gene

Domains & Families for SNORD42B Gene

Gene Families for SNORD42B Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNORD42B: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SNORD42B Gene

Function for SNORD42B Gene

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SNORD42B Gene

Localization for SNORD42B Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for SNORD42B Gene

Pathways & Interactions for SNORD42B Gene

SuperPathways for SNORD42B Gene

No Data Available

Interacting Proteins for SNORD42B Gene

Gene Ontology (GO) - Biological Process for SNORD42B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SNORD42B Gene

Drugs & Compounds for SNORD42B Gene

No Compound Related Data Available

Transcripts for SNORD42B Gene

fRNAdb Secondary structures for SNORD42B Gene

  • FR235088

mRNA/cDNA for SNORD42B Gene

Alternative Splicing Database (ASD) splice patterns (SP) for SNORD42B Gene

No ASD Table

Relevant External Links for SNORD42B Gene

GeneLoc Exon Structure for
SNORD42B
ECgene alternative splicing isoforms for
SNORD42B

Expression for SNORD42B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNORD42B Gene

NURSA nuclear receptor signaling pathways regulating expression of SNORD42B Gene:

SNORD42B
genes like me logo Genes that share expression patterns with SNORD42B: 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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNORD42B Gene

Orthologs for SNORD42B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNORD42B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNORD42 35
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SNORD42 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SNORD42 35
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Snord42b 35
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNORD42 35
  • 75 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SNORD42 35
  • 75 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia SNORD42 35
  • 74 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii SNORD42 35
  • 74 (a)
OneToMany
Species where no ortholog for SNORD42B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SNORD42B Gene

ENSEMBL:
Gene Tree for SNORD42B (if available)
TreeFam:
Gene Tree for SNORD42B (if available)

Paralogs for SNORD42B Gene

No data available for Paralogs for SNORD42B Gene

Variants for SNORD42B Gene

Sequence variations from dbSNP and Humsavar for SNORD42B Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1002162539 -- 28,718,946(+) AACTT(C/G)ACAGT upstream-variant-2KB
rs1002499492 -- 28,719,715(+) TTACA(-/GTGAGCCGAGATCGCGCC)ACTGC upstream-variant-2KB
rs1002511645 -- 28,718,579(+) TGGAA(G/T)CTATC upstream-variant-2KB
rs1002678307 -- 28,720,617(+) TGCAC(A/C)TGTGG intron-variant, downstream-variant-500B, upstream-variant-2KB
rs1002828875 -- 28,721,114(+) TGGGA(G/T)GCCGA intron-variant, downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SNORD42B Gene

Variant ID Type Subtype PubMed ID
nsv1064087 CNV gain 25217958

Relevant External Links for SNORD42B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNORD42B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SNORD42B Gene

Disorders for SNORD42B Gene

Relevant External Links for SNORD42B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNORD42B

No disorders were found for SNORD42B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNORD42B Gene

Publications for SNORD42B Gene

  1. Cloning, sequencing, gene organization, and localization of the human ribosomal protein RPL23A gene. (PMID: 9417910) Fan W. … Lennon G. (Genomics 1997) 2 3 64
  2. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PMID: 19446021) Dieci G. … Montanini B. (Genomics 2009) 3 64
  3. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. (PMID: 16381836) Lestrade L. … Weber M.J. (Nucleic Acids Res. 2006) 1
  4. NONCODE: an integrated knowledge database of non-coding RNAs. (PMID: 15608158) Liu C. … Chen R. (Nucleic Acids Res. 2005) 1
  5. RNAdb--a comprehensive mammalian noncoding RNA database. (PMID: 15608161) Pang K.C. … Mattick J.S. (Nucleic Acids Res. 2005) 1

Products for SNORD42B Gene

Sources for SNORD42B Gene

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