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    ISYNA1 inositol-3-phosphate synthase 1 [ Homo sapiens (human) ]

    Gene ID: 51477, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ISYNA1provided by HGNC
    Official Full Name
    inositol-3-phosphate synthase 1provided by HGNC
    Primary source
    HGNC:HGNC:29821
    See related
    Ensembl:ENSG00000105655 MIM:611670; AllianceGenome:HGNC:29821
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IPS; INO1; INOS; IPS 1; IPS-1
    Summary
    This gene encodes an inositol-3-phosphate synthase enzyme. The encoded protein plays a critical role in the myo-inositol biosynthesis pathway by catalyzing the rate-limiting conversion of glucose 6-phosphate to myoinositol 1-phosphate. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 4. [provided by RefSeq, Nov 2011]
    Expression
    Broad expression in testis (RPKM 72.6), placenta (RPKM 57.0) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ISYNA1 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18434388..18438133, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18568567..18572312, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18545198..18548943, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 3189 Neighboring gene growth differentiation factor 15 Neighboring gene leucine rich repeat containing 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18518971-18519471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10392 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18526865-18527500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10393 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18528379-18528618 Neighboring gene single stranded DNA binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534153-18534654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534655-18535154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541209-18541757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541758-18542305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18546343-18547240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18548168-18549155 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18549156-18550142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18557131-18557659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561006-18561812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561813-18562619 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18566359-18566575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14321 Neighboring gene elongation factor for RNA polymerase II Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18579531-18580168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18587281-18588108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18589364-18590266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594428-18594928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594929-18595429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18596277-18596862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18605831-18606730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18611236-18612222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18618231-18619072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18631869-18632384 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18632385-18632900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18640318-18641203 Neighboring gene Sharpr-MPRA regulatory region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18652136-18652636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10407 Neighboring gene FKBP prolyl isomerase 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. [Clinicopathological significance of ISYNA1 expression in pancreatic ductal adenocarcinoma]. Zhou L, et al. Zhonghua Wai Ke Za Zhi, 2019 Mar 1. PMID 30861650
    2. L-myo-inositol-1-phosphate synthase expressed in developing organ: isolation and characterisation of the enzyme from human fetal liver. Chhetri DR, et al. Appl Biochem Biotechnol, 2012 Aug. PMID 22707096
    3. ISYNA1 is overexpressed in bladder carcinoma and regulates cell proliferation and apoptosis. Guo X, et al. Biochem Biophys Res Commun, 2019 Nov 5. PMID 31495492
    4. cDNA cloning and gene expression analysis of human myo-inositol 1-phosphate synthase. Guan G, et al. Arch Biochem Biophys, 2003 Sep 15. PMID 12941308
    5. E2F1 regulation of the human myo-inositol 1-phosphate synthase (ISYNA1) gene promoter. Seelan RS, et al. Arch Biochem Biophys, 2004 Nov 1. PMID 15464731

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cigarette smoke induces the ROS accumulation and iNOS activation through deactivation of Nrf-2/SIRT3 axis to mediate the human bronchial epithelium ferroptosis.
      Title: Cigarette smoke induces the ROS accumulation and iNOS activation through deactivation of Nrf-2/SIRT3 axis to mediate the human bronchial epithelium ferroptosis.
    2. The myo-inositol biosynthesis rate-limiting enzyme ISYNA1 suppresses the stemness of ovarian cancer via Notch1 pathway.
      Title: The myo-inositol biosynthesis rate-limiting enzyme ISYNA1 suppresses the stemness of ovarian cancer via Notch1 pathway.
    3. Musashi2 promotes the progression of pancreatic cancer through a novel ISYNA1-p21/ZEB-1 pathway.
      Title: Musashi2 promotes the progression of pancreatic cancer through a novel ISYNA1-p21/ZEB-1 pathway.
    4. The ISYNA1 was an important regulatory factors and related networks were involved in multiple functional processes.
      Title: ISYNA1 is overexpressed in bladder carcinoma and regulates cell proliferation and apoptosis.
    5. Abnormal expression of ISYNA1 may play an important role in the progression of pancreatic ductal adenocarcinoma
      Title: [Clinicopathological significance of ISYNA1 expression in pancreatic ductal adenocarcinoma].
    6. analysis of how myo-inositol-3-phosphate synthase is regulated by phosphorylation
      Title: Phosphorylation regulates myo-inositol-3-phosphate synthase: a novel regulatory mechanism of inositol biosynthesis.
    7. MIP synthase expressed in developing fetal liver and shows optima pH between 7.0 and 7.5.
      Title: L-myo-inositol-1-phosphate synthase expressed in developing organ: isolation and characterisation of the enzyme from human fetal liver.
    8. Upregulation occurs through the interaction of several low-affinity E2F binding motifs present in the minimal promoter.
      Title: E2F1 regulation of the human myo-inositol 1-phosphate synthase (ISYNA1) gene promoter.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables inositol-3-phosphate synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol-3-phosphate synthase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables inositol-3-phosphate synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in inositol biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inositol biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inositol biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in phospholipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    inositol-3-phosphate synthase 1
    Names
    MI-1-P synthase
    MIP synthase
    myo-inositol 1-phosphate synthase A1
    testis secretory sperm-binding protein Li 200a
    NP_001164409.1
    NP_001240318.1
    NP_057452.1
    XP_011526361.1
    XP_054177164.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_031809.1 RefSeqGene

      Range
      5169..8914
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001170938.2 → NP_001164409.1  inositol-3-phosphate synthase 1 isoform 2

      See identical proteins and their annotated locations for NP_001164409.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AI983065, AK092179, BC018952, BP392170
      Consensus CDS
      CCDS54234.1
      UniProtKB/TrEMBL
      B3KSG0
      Related
      ENSP00000415458.3, ENST00000457269.8
      Conserved Domains (1) summary
      pfam07994
      Location:34 → 437
      NAD_binding_5; Myo-inositol-1-phosphate synthase

    2. NM_001253389.2 → NP_001240318.1  inositol-3-phosphate synthase 1 isoform 4

      See identical proteins and their annotated locations for NP_001240318.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AI983065, AL137749, BP392170
      Consensus CDS
      CCDS62603.1
      UniProtKB/TrEMBL
      B3KSG0
      Related
      ENSP00000475677.1, ENST00000578963.5
      Conserved Domains (1) summary
      pfam07994
      Location:1 → 363
      NAD_binding_5; Myo-inositol-1-phosphate synthase

    3. NM_016368.5 → NP_057452.1  inositol-3-phosphate synthase 1 isoform 1

      See identical proteins and their annotated locations for NP_057452.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AI983065, AK021526, BP392170
      Consensus CDS
      CCDS12379.1
      UniProtKB/Swiss-Prot
      B3KRT1, G5E9U0, Q6NXT5, Q7Z525, Q9BT65, Q9H2Y2, Q9NPH2, Q9NSU0, Q9NVW7
      UniProtKB/TrEMBL
      A0A140VK73
      Related
      ENSP00000337746.7, ENST00000338128.13
      Conserved Domains (1) summary
      cl00554
      Location:7 → 507
      NAD_binding_5; Myo-inositol-1-phosphate synthase

    RNA

    1. NR_045573.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI983065, AK296022, BP392170

    2. NR_045574.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks two exons in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI983065, AK093461, AL137749, BP392170, DA615868, DB244754
      Related
      ENST00000582811.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      18434388..18438133 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528059.3 → XP_011526361.1  inositol-3-phosphate synthase 1 isoform X1

      Conserved Domains (1) summary
      cl00554
      Location:7 → 575
      NAD_binding_5; Myo-inositol-1-phosphate synthase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      18568567..18572312 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321189.1 → XP_054177164.1  inositol-3-phosphate synthase 1 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001170939.1: Suppressed sequence

      Description
      NM_001170939.1: This RefSeq was permanently suppressed because currently there is insufficient support for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NPH2.1 GenPept UniProtKB/Swiss-Prot:Q9NPH2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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