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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HSDL2 Gene

protein-coding   GIFtS: 51
GCID: GC09P115142

hydroxysteroid dehydrogenase like 2

(Previous name: chromosome 9 open reading frame 99 )
(Previous symbol: C9orf99)
 Explore 5 diseases affiliated with
HSDL2 via our new
 Human Malady Compendium 
Biological research products
for HSDL2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Hydroxysteroid Dehydrogenase Like 21 2     Short Chain Dehydrogenase/Reductase Family 13C, Member 12
C9orf991 2 3     EC 1.-.-.-3
SDR13C11 2     EC 1.1.18
Chromosome 9 Open Reading Frame 991     EC 1.1.1.1008
Hydroxysteroid Dehydrogenase-Like Protein 22     

External Ids:    HGNC: 185721   Entrez Gene: 842632   Ensembl: ENSG000001194717   UniProtKB: Q6YN163   
ORGUL members:         
NONCODE:n410169    

Export aliases for HSDL2 gene to outside databases

Previous GC identifers: GC09P112222 GC09P114182 GC09P084741


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: HSDL2_HUMAN, Q6YN16
Function: Has apparently no steroid dehydrogenase activity




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.1  NT_008470.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HSDL2 gene promoter:
         ER-alpha   COUP-TF1   HSF1 (long)   COUP   HNF-4alpha2   HNF-4alpha1   COUP-TF   HSF1short   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHSDL2 promoter sequence
   Search SABiosciences Chromatin IP Primers for HSDL2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HSDL2


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

Entrez Gene cytogenetic band: 9q32   Ensembl cytogenetic band:  9q32   HGNC cytogenetic band: 9q32

HSDL2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HSDL2 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P115142:  view genomic region     (about GC identifiers)

Start:
115,142,217 bp from pter      End:
115,234,690 bp from pter
Size:
92,474 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HSDL2_HUMAN, Q6YN16 (See protein sequence)
Recommended Name: Hydroxysteroid dehydrogenase-like protein 2  
Size: 418 amino acids; 45395 Da
Subcellular location: Peroxisome
1 PDB 3D structure from and Proteopedia for HSDL2:
3KVO (3D)    
Secondary accessions: A8K1L4 A8K8X1 A8MSV3 Q658M8 Q9BT58
Alternative splicing: 2 isoforms:  Q6YN16-1   Q6YN16-2   

Explore the universe of human proteins at neXtProt for HSDL2: NX_Q6YN16

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6YN16

  • 2 DME Specific Peptides for HSDL2 (Q6YN16)
     SRGIGKA  TGASRGIG 

    HSDL2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001182751.1  NP_115679.2  

    ENSEMBL proteins: 
     ENSP00000381785   ENSP00000381783   ENSP00000262542   ENSP00000442278  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for HSDL2

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--
    GO:0005777peroxisome IDA19703561


    HSDL2 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HSDL2 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR020904 Sc_DH/Rdtase_CS
     IPR002347 Glc/ribitol_DH
     IPR002198 DH_sc/Rdtase_SDR
     IPR016040 NAD(P)-bd_dom
     IPR003033 SCP2_sterol-bd_dom

    Graphical View of Domain Structure for InterPro Entry Q6YN16

    ProtoNet protein and cluster: Q6YN16

    3 Blocks protein families:
    IPB002198 Short-chain dehydrogenase/reductase SDR
    IPB002347 Glucose/ribitol dehydrogenase family signature
    IPB003033 Sterol-binding


    UniProtKB/Swiss-Prot: HSDL2_HUMAN, Q6YN16
    Similarity: Belongs to the short-chain dehydrogenases/reductases (SDR) family
    Similarity: Contains 1 SCP2 domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: HSDL2_HUMAN, Q6YN16
    Function: Has apparently no steroid dehydrogenase activity

    Enzyme Numbers (IUBMB): EC 1.1.1.1002 EC 1.1.12 EC 1.-.-.-1

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    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate HSDL2 (see all 31):
    hsa-miR-323-3p hsa-miR-498 hsa-miR-607 hsa-miR-875-3p hsa-miR-448 hsa-miR-495 hsa-miR-300 hsa-miR-944
    SwitchGear 3'UTR luciferase reporter plasmidHSDL2 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003674molecular_function ND--
    GO:0016491oxidoreductase activity IEA--
    GO:0032934sterol binding IEA--


    HSDL2 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for HSDL2:
     Decreased Wnt reporter activit  Decreased viability  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HSDL2

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

    5/11 Interacting proteins for HSDL2 (Q6YN163 ENSP000003817854) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IKBKEQ141643, ENSP000003560874I2D: score=1 STRING: ENSP00000356087
    ATG10Q9H0Y03I2D: score=1 
    C12orf44Q9BSB43I2D: score=1 
    CLN3Q132863I2D: score=1 
    DDA1Q9BW613I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--


    HSDL2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HSDL2
    Search CenterWatch for drugs/clinical trials and news about HSDL2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HSDL2 gene (2 alternative transcripts): 
    NM_001195822.1  NM_032303.4  

    Unigene Cluster for HSDL2:

    Hydroxysteroid dehydrogenase like 2
    Hs.59486  [show with all ESTs]
    Unigene Representative Sequence: NM_032303
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000398805(uc004bga.2 uc011lwv.2 uc004bgc.2 uc004bgb.2 uc011lww.2)
    ENST00000398803 ENST00000488101 ENST00000467434 ENST00000480881 ENST00000262542
    ENST00000539114

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    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate HSDL2 (see all 31):
    hsa-miR-323-3p hsa-miR-498 hsa-miR-607 hsa-miR-875-3p hsa-miR-448 hsa-miR-495 hsa-miR-300 hsa-miR-944
    SwitchGear 3'UTR luciferase reporter plasmidHSDL2 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK023959.1 AK090940.1 AK098721.1 AK225946.1 AK289929.1 AK292486.1 AK313605.1 AL050130.1 
    AL833735.1 AY093428.1 BC004331.1 BC095451.1 NR_036651.1 

    13 DOTS entries:

    DT.451395  DT.97858811  DT.99929521  DT.121195568  DT.121195638  DT.426506  DT.100037080  DT.100796747 
    DT.121611699  DT.95078502  DT.100841014  DT.92433862  DT.97858812 

    24/321 AceView cDNA sequences (see all 321):

    BX500370 W76436 BM821865 BX439325 AI474529 BM833960 F36769 AA062584 
    AU142060 AL701930 BX280967 AA749291 AI077381 BM712046 BQ086273 AW044490 
    AA211903 CR614573 CA424646 F23449 AK090940 CB115766 BF969827 BQ694534 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for HSDL2 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b
    SP1:                                                                    -                                 
    SP2:                                            -     -                 -                                 
    SP3:                          -                                         -                                 
    SP4:                                -                 -     -           -                                 
    SP5:                          -                       -                 -                                 


    ECgene alternative splicing isoforms for HSDL2

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HSDL2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AATCGCTAAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See HSDL2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HSDL2

    SOURCE GeneReport for Unigene cluster: Hs.59486

    UniProtKB/Swiss-Prot: HSDL2_HUMAN, Q6YN16
    Tissue specificity: Ubiquitous

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    In Situ
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    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HSDL2 gene from 6/25 species (see all 25)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves LOC1008580571 hydroxysteroid dehydrogenase-like protein 2-like 73.04(n)
    73.12(a)
      100858057  XM_003643092.1  XP_003643140.1 
    lizard
    (Anolis carolinensis)
    Reptilia HSDL26
    --
    71(a)
    1 ↔ 1
    2(57682461-57707281)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC684982 hypothetical protein MGC68498 75.62(n)    BC059996.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb58f082 wufb58f08 74.18(n)   322347  BC062838.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG55901 CG5590 57.4(n)
    59.06(a)
      43325  NM_143321.2  NP_651578.1 
    worm
    (Caenorhabditis elegans)
    Secernentea dhs-181 Protein DHS-18 60.61(n)
    65.45(a)
      179529  NM_073411.4  NP_505812.1 


    ENSEMBL Gene Tree for HSDL2 (if available)
    TreeFam Gene Tree for HSDL2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HSDL2 gene
    SCP22  HSD17B42  SCP2D12  
    1 SIMAP similar gene for HSDL2 using alignment to 3 protein entries:     HSDL2_HUMAN (see all proteins):
    SCP2

    HSDL2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1786 NCBI SNPs in HSDL2 are shown (see all 1786    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs113138531,2
    C,--84816212(+) ACAAAC/-CTTTT 1 -- int11Minor allele frequency- -:0.50CSA 2
    rs759304131,2
    --115140208(+) CATTTC/TTACTA 3 -- us2k11Minor allele frequency- T:0.01NA 120
    rs49791091,2
    C,F,A,H,--115140276(+) AAATGG/ACTTCT 3 -- us2k126Minor allele frequency- A:0.34NS EA NA WA CSA 2563
    rs793702841,2
    C,--115140390(+) CTCTC-/CTTCTTCA 3 -- us2k10--------
    rs2020760271,2
    --115140393(+) TCCTT-/CTCCACCC 3 -- us2k10--------
    rs1431905341,2
    --115140458(+) AAGGTA/CATGGG 3 -- us2k10--------
    rs1854529711,2
    --115140500(+) GTCAAA/CGTACT 3 -- us2k10--------
    rs743995221,2
    --115140527(+) AACTTG/CCTTGG 3 -- us2k12Minor allele frequency- C:0.09CSA WA 120
    rs1906589961,2
    --115140531(+) TGCTTA/GGTAAA 3 -- us2k10--------
    rs1814803131,2
    --115140588(+) TCGCAA/CAGTAT 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for HSDL2 (115142217 - 115234690 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for HSDL2
         1 CNV: 96255
         1 Indel: 96256

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HSDL2
    DNA2.0 Custom Variant and Variant Library Synthesis for HSDL2

    (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.)
    About This Section

    HSDL2 for disorders           About GeneDecksing

    5 diseases for HSDL2:    About MalaCards
    cleft lip/palate    cleft lip    atherosclerosis    tuberculosis
    mycobacterium tuberculosis

    Human Genome Epidemiology (HuGE) Navigator: HSDL2 (2 documents)

    Export disorders for HSDL2 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)
    About This Section

    PubMed articles for HSDL2 gene, integrated from 9 sources (see all 17):
    (articles sorted by number of sources associating them with HSDL2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of a novel human hydroxysteroid dehydrogenase-like 2 (HSDL2) cDNA from fetal brain. (PubMed id 12834046)1, 2, 3, 9 Dai J.... Mao Y. (2003)
    2. In search for function of two human orphan SDR enzymes: Hydroxysteroid dehydrogenase like 2 (HSDL2) and short-chain dehydrogenase/reductase-orphan (SDR-O). (PubMed id 19703561)1, 2, 9 Kowalik D.... Moeller G. (2009)
    3. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PubMed id 19027726)1, 3 Persson B.... Oppermann U. (2009)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. (PubMed id 20583170)1 Letra A....Vieira A.R. (2010)
    9. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (2010)
    10. Transcriptional profiling uncovers a network of chole sterol-responsive atherosclerosis target genes. (PubMed id 18369455)1 Skogsberg J....BjAPrkegren J. (2008)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84263 HGNC: 18572 AceView: C9orf99 Ensembl:ENSG00000119471 euGenes: HUgn84263
    ECgene: HSDL2 H-InvDB: HSDL2

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HSDL2 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 HSDL2 gene:
    Search GeneIP for patents involving HSDL2

    GeneCards and IP:
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