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SERF1B Gene

protein-coding   GIFtS: 41
GCID: GC05P069322

Small EDRK-Rich Factor 1B (Centromeric)

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Small EDRK-Rich Factor 1B (Centromeric)1 2     H4F5C2
Protein 4F52 3     Small EDRK-Rich Factor 12
FAM2B2 3     FAM2A3
h4F52 3     SERF13
SMA Modifier 12 3     SMAM13

External Ids:    HGNC: 107561   Entrez Gene: 7284922   Ensembl: ENSG000002055727   UniProtKB: O759203   

Export aliases for SERF1B gene to outside databases

Previous GC identifers: GC05M069157 GC05M035205 GC05P069810 GC05P069856 GC05P069857 GC05P070232 GC05U900528 GC05P069358 GC05P065845


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SERF1B Gene:
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least
four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and
complexity of the sequence have also caused difficulty in determining the organization of this genomic region.
This gene is the centromeric copy which is identical to the telomeric copy. Alternatively spliced transcripts
have been documented but it is unclear whether alternative splicing occurs for both the centromeric and telomeric
copies of the gene. The gene encodes a protein of unknown function which bears low-level homology with the
RNA-binding domain of matrin-cyclophilin, a protein which colocalizes with small nuclear ribonucleoproteins
(snRNPs) and the SMN1 gene product. (provided by RefSeq, Jul 2008)

GeneCards Summary for SERF1B Gene:
SERF1B (small EDRK-rich factor 1B (centromeric)) is a protein-coding gene. An important paralog of this gene is SERF1A.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000005.9  NC_018916.2  NT_034772.7  NT_187651.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the SERF1B gene promoter:
         Nkx2-2   CUTL1   IRF-2   POU2F1   FOXJ2 (long isoform)   POU2F1a   Chx10   STAT3   FOXJ2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSERF1B promoter sequence
   Search Chromatin IP Primers for SERF1B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SERF1B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q13.2   Ensembl cytogenetic band:  5q13.2   HGNC cytogenetic band: 5q13

SERF1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SERF1B gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P069322:  view genomic region     (about GC identifiers)

Start:
69,321,074 bp from pter      End:
69,338,940 bp from pter
Size:
17,867 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SERF1_HUMAN, O75920 (See protein sequence)
Recommended Name: Small EDRK-rich factor 1  
Size: 110 amino acids; 12349 Da
Secondary accessions: B7ZKM2 O75919 Q52LK5
Alternative splicing: 2 isoforms:  O75920-1   O75920-2   

Explore the universe of human proteins at neXtProt for SERF1B: NX_O75920

Explore proteomics data for SERF1B at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SERF1B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001171558.1  NP_075267.1  

    ENSEMBL proteins: 
     ENSP00000370127   ENSP00000370126   ENSP00000423882   ENSP00000421563   ENSP00000427181  

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    Novus Biologicals SERF1B Lysate
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SERF1B

     
    Search eBioscience for Proteins for SERF1B 

     
    antibodies-online proteins for SERF1B (5 products) 

     
    antibodies-online peptides for SERF1B

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    antibodies-online antibodies for SERF1B (8 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR007513 Uncharacterised_SERF

    Graphical View of Domain Structure for InterPro Entry O75920

    ProtoNet protein and cluster: O75920

    1 Blocks protein domain: IPB007513 Four F5 protein

    UniProtKB/Swiss-Prot: SERF1_HUMAN, O75920
    Similarity: Belongs to the SERF family


    Find genes that share domains with SERF1B           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with SERF1B           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for SERF1B:
     Decreased viability with pacli  Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SERF1B

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    2 qRT-PCR Assays for microRNAs that regulate SERF1B:
    hsa-miR-561 hsa-miR-488
    SwitchGear 3'UTR luciferase reporter plasmidSERF1B 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SERF1B

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    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol1
    nucleus1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    Find genes that share ontologies with SERF1B           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SERF1B
    Interactions:

        Search GeneGlobe Interaction Network for SERF1B

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for SERF1B (O759203 ENSP000003701264) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PIK3R3Q925693, ENSP000002627414I2D: score=2 STRING: ENSP00000262741
    PRPF8ENSP000003043504STRING: ENSP00000304350
    SNRNP200ENSP000003171234STRING: ENSP00000317123
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007399nervous system development TAS9731538

    Find genes that share ontologies with SERF1B           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SERF1B (SERF1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SERF1B gene (2 alternative transcripts): 
    NM_001178087.1  NM_022978.2  

    Unigene Cluster for SERF1B:

    Small EDRK-rich factor 1B (centromeric)
    Hs.559428  [show with all ESTs]
    Unigene Representative Sequence: NM_022978
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380751(uc003jxz.3) ENST00000380750(uc003jyb.3) ENST00000503931
    ENST00000506542 ENST00000515588 ENST00000507177 ENST00000514285 ENST00000513144

    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate SERF1B:
    hsa-miR-561 hsa-miR-488
    SwitchGear 3'UTR luciferase reporter plasmidSERF1B 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SERF1B
    Predesigned siRNA for gene silencing in human, mouse, rat SERF1B
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    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SERF1B
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SERF1B
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SERF1B
      QuantiFast Probe-based Assays in human, mouse, rat SERF1B

    Additional mRNA sequence: 

    BC101970.1 BC103687.1 BC104738.1 BC143255.1 BC143260.1 BC171749.1 

    15 DOTS entries:

    DT.214248  DT.95157164  DT.120845327  DT.92420310  DT.99985956  DT.453238  DT.120845152  DT.75118279 
    DT.101982577  DT.97762404  DT.97780241  DT.99975805  DT.100822322  DT.40264383  DT.97770443 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SERF1B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SERF1B Expression
    About this image

    SERF1B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SERF1B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.559428

    UniProtKB/Swiss-Prot: SERF1_HUMAN, O75920
    Tissue specificity: Isoform Long is predominantly expressed in heart, brain and skeletal muscle. Isoform Short and
    Isoform Long are expressed throughout the central nervous system, including spinal cord

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SERF1B

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for SERF1B gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Serf11 small EDRK-rich factor 1 89.78(n)
    93.55(a)
      20365  NM_011353.2  NP_035483.1 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    58(a)
    1 → many
    Z(72863015-72869682)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    50(a)
    1 → many
    4(131135278-131135466)
    zebrafish
    (Danio rerio)
    Actinopterygii serf26
    si:ch211-39k3.26
    si:ch211-39k3.2
    48(a)
    46(a)
    many ↔ many
    many ↔ many
    7(31612032-31617442) ENSDARG00000074340
    18(25536287-25538613) ENSDARG00000075881


    ENSEMBL Gene Tree for SERF1B (if available)
    TreeFam Gene Tree for SERF1B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SERF1B gene
    SERF1A1 2  
    Selected SIMAP similar genes for SERF1B using alignment to 3 protein entries:     SERF1_HUMAN (see all proteins) (see all similar genes):
    SERF1A    ZNF738    SERF2    IFT122    IPO7    MKRN1
    ZNF83    NSD1    CNOT2    KLHDC1    NDUFS7    SUMF2
    FANCA    HGSNAT    DAW1    LRRC36    SCLT1    C15orf40

    Find genes that share paralogs with SERF1B           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SERF1B (see all 18)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3724080641,2
    C--70230451(-) AGCCCA/GTAGTC 1 -- ds50010--------
    rs1879553451,2
    --70232659(-) CTGAAA/CTAACC 1 -- int10--------
    rs1835076391,2
    C--70232672(-) CAGTCC/TCATTC 1 -- int10--------
    rs1912249791,2
    --70233040(-) TTTATA/GTATCT 1 -- int10--------
    rs2018675701,2
    C--70237398(-) CACACA/TCACAC 1 -- int10--------
    rs2008950781,2
    C--70238343(-) AGAATA/GATTGT 1 -- int10--------
    rs1871142401,2
    --70238636(-) TTTTTA/TTTTTT 1 -- int10--------
    rs1824903771,2
    --70238639(-) TTATTA/TTTTTT 1 -- int10--------
    rs715769331,2
    C--70244861(-) TCTTAC/TTCTGT 2 -- int12Minor allele frequency- T:0.00NA 4
    rs802974991,2
    ----70237396(-) CACACT/ACACTC 1 -- int11Minor allele frequency- A:0.50NA 2

    HapMap Linkage Disequilibrium report for SERF1B (69321074 - 69338940 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SERF1B (see all 91):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv471432CNV Duplication19718026
    dgv19n31CNV Duplication19718026
    nsv471547CNV Duplication19718026
    dgv6149n71CNV Loss21882294
    dgv6089n71CNV Loss21882294
    nsv881768CNV Loss21882294
    dgv6144n71CNV Loss21882294
    nsv821643CNV Loss15273396
    dgv6138n71CNV Loss21882294
    dgv6101n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SERF1B
    DNA2.0 Custom Variant and Variant Library Synthesis for SERF1B

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases from the University of Copenhagen DISEASES database for SERF1B:
    Scrapie     Spinal muscular atrophy

    Find genes that share disorders with SERF1B           About GenesLikeMe


    Export disorders for SERF1B gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SERF1B gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SERF1B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Identification of a candidate modifying gene for spinal muscular atrophy by comparative genomics. (PubMed id 9731538)1, 2 Scharf J.M.... Kunkel L.M. (Nat. Genet. 1998)
    3. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    4. Gene expression profile of the human trabecular meshwork: NEIBank sequence tag analysis. (PubMed id 12766061)1 Tomarev S.I....Malyukova I. (amp 2003)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. Comparative sequence analysis of the mouse and human Lgn1/SMA interval. (PubMed id 10486205)1 Endrizzi M....Dietrich W.F. (Genomics 1999)
    7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 728492 HGNC: 10756 Ensembl:ENSG00000205572 euGenes: HUgn728492 ECgene: SERF1B
    H-InvDB: SERF1B

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SERF1B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SERF1B gene:
    Search GeneIP for patents involving SERF1B

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