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Aliases for SNORD88B Gene

Subcategory (RNA class) for SNORD88B Gene

snoRNA

Quality Score for this RNA gene is

7

Aliases for SNORD88B Gene

  • Small Nucleolar RNA, C/D Box 88B 2 3 5
  • HBII-180B 3

External Ids for SNORD88B Gene

ORGUL Members for SNORD88B Gene

Previous GeneCards Identifiers for SNORD88B Gene

  • GC19U900585
  • GC19M055996
  • GC19M051302
  • GC19M047636

Summaries for SNORD88B Gene

GeneCards Summary for SNORD88B Gene

SNORD88B (Small Nucleolar RNA, C/D Box 88B) is an RNA Gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORD88B Gene - the ORGUL cluster for this gene includes several descriptions:

  • 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 SNORD88: The members of this family belong to the C/D class of snoRNAs which contain the 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 [1]. This family includes mouse MBII-211 and MBII-180 identified in [2] and the human orthologue HBII-180 (SNORD88). HBII-180 is predicted to guide the 2'O-ribose methylation of 28S rRNA C3680 [3].

View fRNAdb secondary structures for SNORD88B

Additional gene information for SNORD88B Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SNORD88B Gene

Genomics for SNORD88B Gene

GeneHancer (GH) Regulatory Elements for SNORD88B Gene

Promoters and enhancers for SNORD88B 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
GH19I050720 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 10.9 +75.8 75769 5.7 HDGF SIN3A ZNF2 ZBTB7B POLR2B CBX5 E2F8 FOS KLF13 SP3 CLEC11A C19orf48 GPR32 AKT1S1 SNORD88A SNORD88B SNORD88C LINC01869 NUP62 KLK1
GH19I050835 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.1 -37.1 -37122 1.7 HDGF PKNOX1 ATF1 ARNT SIN3A FEZF1 GLI4 ZNF48 ZNF121 POLR2B KLK15 ZNF175 NUP62 PTOV1-AS2 LINC01869 SNORD88C C19orf48 KLK2 SNORD88A SNORD88B
GH19I050537 Enhancer 1.1 ENCODE dbSUPER 11.1 +261.2 261246 0.1 SIN3A ZNF2 IRF4 ZNF48 ARID2 ZNF143 ATF7 REST ZNF592 MEF2D ASPDH JOSD2 LRRC4B GPR32 SNORD88A SNORD88B SNORD88C NAPSA NR1H2 C19orf48
GH19I050727 Enhancer 1.1 Ensembl ENCODE 10.9 +70.6 70643 1.3 HDGF PKNOX1 ATF1 POLR2B CBX5 ZNF143 FOS ATF7 SP3 NCOA1 GPR32 SNORD88A SNORD88B SNORD88C C19orf48 LINC01869 KLK1 KLK15 FUZ CLEC11A
GH19I050538 Enhancer 0.9 dbSUPER 11.1 +261.7 261687 0.7 HDAC1 RB1 ZSCAN4 SIN3A ZNF2 IRF4 THRB RAD21 ZEB1 ARID2 ASPDH JOSD2 LRRC4B GPR32 SNORD88A SNORD88B SNORD88C NAPSA NR1H2 C19orf48
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SNORD88B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNORD88B gene promoter:

Genomic Locations for SNORD88B Gene

Genomic Locations for SNORD88B Gene
chr19:50,799,029-50,799,125
(GRCh38/hg38)
Size:
97 bases
Orientation:
Minus strand
chr19:51,302,286-51,302,382
(GRCh37/hg19)

Genomic View for SNORD88B Gene

Genes around SNORD88B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNORD88B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNORD88B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNORD88B Gene

ORGUL Member Location for SNORD88B Gene

ORGUL Member Location for SNORD88B gene

Proteins for SNORD88B Gene

Post-translational modifications for SNORD88B Gene

No Post-translational modifications

No data available for DME Specific Peptides for SNORD88B Gene

Domains & Families for SNORD88B Gene

Gene Families for SNORD88B Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNORD88B: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SNORD88B Gene

Function for SNORD88B Gene

Phenotypes From GWAS Catalog for SNORD88B Gene

Animal Model Products

Clone 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 SNORD88B Gene

Localization for SNORD88B Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SNORD88B Gene

Pathways & Interactions for SNORD88B Gene

SuperPathways for SNORD88B Gene

No Data Available

Interacting Proteins for SNORD88B Gene

Gene Ontology (GO) - Biological Process for SNORD88B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SNORD88B Gene

Drugs & Compounds for SNORD88B Gene

No Compound Related Data Available

Transcripts for SNORD88B Gene

fRNAdb Secondary structures for SNORD88B Gene

  • RF00604;SNORD88;AEKP01104557.1/9673-9583

mRNA/cDNA for SNORD88B Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNORD88B Gene

No ASD Table

Relevant External Links for SNORD88B Gene

GeneLoc Exon Structure for
SNORD88B
ECgene alternative splicing isoforms for
SNORD88B

Expression for SNORD88B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNORD88B Gene

mRNA differential expression in normal tissues according to GTEx for SNORD88B Gene

This gene is overexpressed in Prostate (x7.1).

NURSA nuclear receptor signaling pathways regulating expression of SNORD88B Gene:

SNORD88B
genes like me logo Genes that share expression patterns with SNORD88B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 SNORD88B Gene

Orthologs for SNORD88B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNORD88B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNORD88 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SNORD88 34
  • 88 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SNORD88 34
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNORD88 34
  • 79 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SNORD88 34
  • 78 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Gm25108 34
  • 69 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SNORD88 34
  • 53 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia SNORD88 34
  • 66 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii SNORD88 34
  • 59 (a)
OneToMany
Species where no ortholog for SNORD88B 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)
  • 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 SNORD88B Gene

ENSEMBL:
Gene Tree for SNORD88B (if available)
TreeFam:
Gene Tree for SNORD88B (if available)

Paralogs for SNORD88B Gene

No data available for Paralogs for SNORD88B Gene

Variants for SNORD88B Gene

Sequence variations from dbSNP and Humsavar for SNORD88B Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000507527 -- 50,800,465(-) G/A upstream_transcript_variant
rs1000823791 -- 50,800,676(-) A/C upstream_transcript_variant
rs1004156871 -- 50,799,342(-) TC/ upstream_transcript_variant
rs1006317308 -- 50,799,736(-) C/T upstream_transcript_variant
rs1006894604 -- 50,799,180(-) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SNORD88B Gene

Variant ID Type Subtype PubMed ID
dgv203n21 CNV loss 19592680
nsv1140251 OTHER inversion 24896259

Additional Variant Information for SNORD88B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNORD88B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SNORD88B Gene

Disorders for SNORD88B Gene

Additional Disease Information for SNORD88B

No disorders were found for SNORD88B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNORD88B Gene

Publications for SNORD88B Gene

  1. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. (PMID: 11387227) Hüttenhofer A … Brosius J (The EMBO journal 2001) 1 2 3 58
  2. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PMID: 19446021) Dieci G … Montanini B (Genomics 2009) 3 58
  3. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. (PMID: 16381836) Lestrade L … Weber MJ (Nucleic acids research 2006) 1
  4. RNAdb--a comprehensive mammalian noncoding RNA database. (PMID: 15608161) Pang KC … Mattick JS (Nucleic acids research 2005) 1
  5. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. (PMID: 8764399) Nicoloso M … Bachellerie JP (Journal of molecular biology 1996) 1

Products for SNORD88B Gene

Sources for SNORD88B Gene

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