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

SBSPON Gene

protein-coding   GIFtS: 38
GCID: GC08M073977

Somatomedin B And Thrombospondin, Type 1 Domain Containing

(Previous name: chromosome 8 open reading frame 84)
(Previous symbol: C8orf84)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Somatomedin B And Thrombospondin, Type 1 Domain Containing1 2     RPESP2 3
C8orf841 2 3     Chromosome 8 Open Reading Frame 841
RPE Spondin1 2     rpe-spondin1
RPE-spondin2 3     Somatomedin-B And Thrombospondin Type-1 Domain-Containing Protein2

External Ids:    HGNC: 303621   Entrez Gene: 1578692   Ensembl: ENSG000001647647   UniProtKB: Q8IVN83   

Export aliases for SBSPON gene to outside databases


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

GeneCards Summary for SBSPON Gene: 
SBSPON (somatomedin B and thrombospondin, type 1 domain containing) is a protein-coding gene. Diseases associated with SBSPON include choroiditis, and crohn's disease. GO annotations related to this gene include scavenger receptor activity and polysaccharide binding.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000008.10  NT_008183.19  NC_018919.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SBSPON
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSBSPON promoter sequence
   Search SABiosciences Chromatin IP Primers for SBSPON

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


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

Entrez Gene cytogenetic band: 8q21.11   Ensembl cytogenetic band:  8q21.11   HGNC cytogenetic band: 8q21.11

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

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M073977:  view genomic region     (about GC identifiers)

Start:
73,976,775 bp from pter      End:
74,036,323 bp from pter
Size:
59,549 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SBSPO_HUMAN, Q8IVN8 (See protein sequence)
Recommended Name: Somatomedin-B and thrombospondin type-1 domain-containing protein precursor  
Size: 264 amino acids; 29610 Da
Subcellular location: Secreted, extracellular space, extracellular matrix
Sequence caution: Sequence=AAH42877.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAK83466.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAF85659.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A8KAA5 Q96J64

Explore the universe of human proteins at neXtProt for SBSPON: NX_Q8IVN8

Explore proteomics data for SBSPON at MOPED 

SBSPON Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

SBSPON Protein Expression

REFSEQ proteins: NP_694957.3  
ENSEMBL proteins: 
 ENSP00000297354  

Human Recombinant Protein Products for SBSPON: 
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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005578proteinaceous extracellular matrix IEA--
GO:0031012colocalizes with extracellular matrix IDA--

SBSPON for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
2 InterPro protein domains:
 IPR000884 Thrombospondin_1_rpt
 IPR001212 Somatomedin_B_dom

Graphical View of Domain Structure for InterPro Entry Q8IVN8

ProtoNet protein and cluster: Q8IVN8

UniProtKB/Swiss-Prot: SBSPO_HUMAN, Q8IVN8
Similarity: Belongs to the thrombospondin family
Similarity: Contains 1 SMB (somatomedin-B) domain
Similarity: Contains 1 TSP type-1 domain


SBSPON for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005044scavenger receptor activity IEA--
GO:0030247polysaccharide binding IEA--
     
SBSPON for ontologies           About GeneDecksing


Phenotypes:
     3 GenomeRNAi human phenotypes for SBSPON:
 Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 

Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for SBSPON 
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miRNA
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Inhib. RNA
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

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

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

GO IDQualified GO termEvidencePubMed IDs
GO:0006955immune response IEA--

SBSPON for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SBSPON (SBSPO)

Search CenterWatch for drugs/clinical trials and news about SBSPON / SBSPO

(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,
Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SBSPON gene: 
NM_153225.3  

Unigene Cluster for SBSPON:

Somatomedin B and thrombospondin, type 1 domain containing
Hs.439040  [show with all ESTs]
Unigene Representative Sequence: NM_153225
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000297354(uc003xzf.3) ENST00000519697
miRNA
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Inhib. RNA
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QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SBSPON
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                     Customized lentivirus expression plasmids for stable overexpression of SBSPON 
Primer
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SBSPON

Additional mRNA sequence: 

AF087977.1 AK292970.1 AL080094.1 AY040546.1 BC042877.1 

4 DOTS entries:

DT.211522  DT.100778889  DT.100778892  DT.100712381 

24/77 AceView cDNA sequences (see all 77):

BQ182470 H88831 CA413403 BX089861 AF087977 BC042877 NM_153225 CR592835 
AI217135 H88832 AL697631 CR616775 BX324902 BQ024333 AI565404 CR594707 
BQ448226 AA939100 BX382762 AW662355 AI953728 BI764857 BE695858 AA620812 

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™, 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

SBSPON expression in normal human tissues (normalized intensities)      SBSPON embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SBSPON Expression
About this image


SBSPON expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/3 selected tissues (see all 3) fully expand
 
 Umbilical Cord (Extraembryonic Tissues)
         Wharton's jelly-derived stem cells
 
 Intermediate Mesoderm (Gastrulation Derivatives)
         Mesonephros
 
 Bone (Muscoskeletal System)
         Zeugopod Epiphyseal End

See SBSPON Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SBSPON

SOURCE GeneReport for Unigene cluster: Hs.439040

UniProtKB/Swiss-Prot: SBSPO_HUMAN, Q8IVN8
Tissue specificity: Detected in aorta extracellular matrix (at protein level)

    SABiosciences Custom PCR Arrays for SBSPON
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QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SBSPON
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBSPON

(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 SBSPON gene from 6/13 species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Sbspon5
Gm1061
predicted gene 1061, 5 87.63(n)1
89.39(a)1
  1 (4.89 cM)5
2268661  NM_001033288.31  NP_001028460.11 
 158538625 
chicken
(Gallus gallus)
Aves SBSPON1 somatomedin B and thrombospondin, type 1 domain containing 71.92(n)
67.32(a)
  420181  XM_429743.3  XP_429743.3 
lizard
(Anolis carolinensis)
Reptilia SBSPON6
Uncharacterized protein
63(a)
1 ↔ 1
4(33393157-33407503)
zebrafish
(Danio rerio)
Actinopterygii LOC1001512181 RPE-spondin-like 62.18(n)
60.08(a)
  100151218  XM_001920112.1  XP_001920147.1 
fruit fly
(Drosophila melanogaster)
Insecta CG423396
--
19(a)
1 ↔ 1
X(10861755-10933934)
worm
(Caenorhabditis elegans)
Secernentea R17.36
Protein R17.3
15(a)
1 ↔ 1
III(10835014-10839176)


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for SBSPON gene

SBSPON for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for SBSPON
PGOHUM00000259647


(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) 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

10/640 SNPs in SBSPON are shown (see all 640)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs667603821,2
C--73976308(+) TATGG-/TCTTT 
        
TCTTT
1 -- int12Minor allele frequency- TCTTT:0.25NA CSA 4
rs2013517421,2
C--73976311(+) GGTCTG/TTTCTT 1 -- int10--------
rs1884936971,2
--73976446(+) ACCCCA/GTATTA 1 -- int10--------
rs788653081,2
C,F--73976472(+) TTATTC/ATGGTT 1 -- int11Minor allele frequency- A:0.09WA 118
rs746672871,2
C,F--73976501(+) ATTTGC/GTTTCA 1 -- int14Minor allele frequency- G:0.14NA CSA EA 244
rs582080701,2
C--73976509(+) TCAATC/AGTAAA 1 -- int12Minor allele frequency- A:0.11WA 120
rs1930826981,2
C--73976518(+) AAAAAA/CATTAT 1 -- int10--------
rs1502621501,2
C--73976681(+) CTCACA/GGTGCT 1 -- int10--------
rs1389453261,2
--73976712(+) CTCAGA/GAGGCC 1 -- int10--------
rs613283281,2
C,F--73976876(+) ACTTTA/TAATTA 1 -- ut312Minor allele frequency- T:0.11WA 120

HapMap Linkage Disequilibrium report for SBSPON (73976775 - 74036323 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SBSPON: --
SABiosciences Cancer Mutation PCR Assays
SeqTarget long-range PCR primers for resequencing SBSPON
DNA2.0 Custom Variant and Variant Library Synthesis for SBSPON

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
3 diseases for SBSPON:    About MalaCards
choroiditis    crohn's disease    retinitis


SBSPON for disorders           About GeneDecksing


Export disorders for SBSPON 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 SBSPON gene integrated from 9 sources:
(articles sorted by number of sources associating them with SBSPON)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Expressed sequence tag analysis of human RPE/choroid for the NEIBank project: over 6000 non-redundant transcripts, novel genes and splice variants. (PubMed id 12107410)1, 2, 3 Wistow G.... Peterson K. (2002)
  2. Proteomics characterization of extracellular space components in the human aorta. (PubMed id 20551380)1, 2 Didangelos A.... Mayr M. (2010)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  4. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PubMed id 22412388)1 Kenny E.E....Peter I. (2012)
  5. Genetic variants near PDGFRA are associated with corne al curvature in Australians. (PubMed id 22969067)1 Mishra A....Mackey D.A. (2012)
  6. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (2006)
  7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
  8. 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. (2002)
  9. Identifying differentially expressed genes in the mammalian retina and the retinal pigment epithelium by suppression subtractive hybridization. (PubMed id 15218245)9 Schulz H.L....Weber B.H.F. (2004)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 157869 HGNC: 30362 AceView: RPESP Ensembl:ENSG00000164764 euGenes: HUgn157869
ECgene: SBSPON H-InvDB: SBSPON

(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 SBSPON Pharmacogenomics, SNPs, Pathways

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

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 GenScript Custom Purified and Recombinant Proteins Services for SBSPON GenScript Custom cDNA clones with any tag delivered in your preferred vector Services for SBSPON
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 Novus Tissue Slides
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 Gene Synthesis
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBSPON
 SwitchGear 3'UTR luciferase reporter plasmids for SBSPON
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SBSPON
 inGenious Targeting Laboratory - Custom generated mouse model solutions for SBSPON
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Customized transgenic rodents for:
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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(GIFtS: 73)
transforming growth factor, beta 1
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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