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    CRYBG1 crystallin beta-gamma domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 202, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CRYBG1provided by HGNC
    Official Full Name
    crystallin beta-gamma domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:356
    See related
    Ensembl:ENSG00000112297 MIM:601797; AllianceGenome:HGNC:356
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ST4; AIM1
    Summary
    Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in esophagus (RPKM 35.8), skin (RPKM 27.1) and 19 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    6q21
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (106360717..106572017)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107536848..107748164)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106808592..107019892)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene autophagy related 5 Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106770796-106771296 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106771297-106771797 Neighboring gene RNA, U6 small nuclear 344, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106808598-106809464 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106895745-106896246 Neighboring gene uncharacterized LOC105377924 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:106908781-106909430 Neighboring gene RNA, 5S ribosomal pseudogene 211 Neighboring gene uncharacterized LOC101927405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106957727-106958332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106959060-106960018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17433 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:106967140-106968339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107023180-107023700 Neighboring gene MPRA-validated peak6003 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:107033226-107033920 Neighboring gene reticulon 4 interacting protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:107061294-107061801 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:107062309-107062815 Neighboring gene RNA, U6 small nuclear 527, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24893 Neighboring gene ribosomal protein L21 pseudogene 65 Neighboring gene glutaminyl-tRNA amidotransferase subunit QRSL1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein. Scholl ZN, et al. J Biol Chem, 2016 Aug 26. PMID 27378818, Free PMC Article
    2. AIM1 and LINE-1 epigenetic aberrations in tumor and serum relate to melanoma progression and disease outcome. Hoshimoto S, et al. J Invest Dermatol, 2012 Jun. PMID 22402438, Free PMC Article
    3. AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy. Rosenbaum E, et al. Prostate, 2012 Jul 1. PMID 22127895, Free PMC Article
    4. Exploring the limits of sequence and structure in a variant betagamma-crystallin domain of the protein absent in melanoma-1 (AIM1). Aravind P, et al. J Mol Biol, 2008 Sep 5. PMID 18582473, Free PMC Article
    5. Crystallization and preliminary X-ray crystallographic investigations on a betagamma-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens. Aravind P, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2006 Mar 1. PMID 16511323, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a betagamma-Crystallin Protein.
      Title: Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein.
    2. Both DNMT1 and AIM1 show maternal allele-specific methylation and paternal allele-specific transcription.
      Title: DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation.
    3. AIM1, ERGIC1, and TPX2 were shown to be highly expressed especially in prostate cancer tissues, and high mRNA expression of ERGIC1 and TMED3 associated with AR and ERG oncogene expression
      Title: High-throughput transcriptomic and RNAi analysis identifies AIM1, ERGIC1, TMED3 and TPX2 as potential drug targets in prostate cancer.
    4. Methylation status of AIM1 in the prostate cancer specimen may predict for time to recurrence in Gleason 3 + 4 = 7 patients undergoing prostatectomy.
      Title: AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy.
    5. AIM1 promoter hypermethylation was found in higher frequency (P = 0.005) in metastatic melanoma (65%) than in primary melanomas (38%).
      Title: AIM1 and LINE-1 epigenetic aberrations in tumor and serum relate to melanoma progression and disease outcome.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Confirmation of genomewide association signals in Chinese Han population reveals risk loci for ischemic stroke.
    8. tumor-promoting effect of deletion in 6q21, that included genes PRDM1, ATG5 and AIM1
      Title: Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies.
    9. Absent in melanoma 1 (AIM1), an unusual member of the superfamily , contains 12 betagamma-crystallin motifs in six domains. Some of these motifs diverge considerably from the canonical motif sequence. AIM1g1, the first betagamma-crystallin domain of AIM1.
      Title: Exploring the limits of sequence and structure in a variant betagamma-crystallin domain of the protein absent in melanoma-1 (AIM1).
    10. the structure of AIM1g1, a single betagamma-crystallin domain from the protein absent in melanoma 1, was determined
      Title: Crystallization and preliminary X-ray crystallographic investigations on a betagamma-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens.
    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
    A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release.
    EBI GWAS Catalog
    Genome-wide association with select biomarker traits in the Framingham Heart Study.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    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)

    Genotypes

    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 carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    beta/gamma crystallin domain-containing protein 1
    Names
    absent in melanoma 1 protein
    beta-gamma crystallin domain containing 1
    suppression of tumorigenicity 4 (malignant melanoma)

    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.

    mRNA and Protein(s)

    1. NM_001371242.2 → NP_001358171.1  beta/gamma crystallin domain-containing protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL109920, AL359292, AL390074
      Consensus CDS
      CCDS93984.1
      UniProtKB/TrEMBL
      A0A0J9YWL0
      Related
      ENSP00000488010.2, ENST00000633556.3
      Conserved Domains (4) summary
      smart00247
      Location:1431 → 1522
      XTALbg; Beta/gamma crystallins
      PHA03307
      Location:192 → 621
      PHA03307; transcriptional regulator ICP4; Provisional
      cd00161
      Location:1997 → 2125
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam00030
      Location:1627 → 1720
      Crystall; Beta/Gamma crystallin

    2. NM_001624.4 → NP_001615.2  beta/gamma crystallin domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001615.2

      Status: VALIDATED

      Source sequence(s)
      AL359292, AL390074
      UniProtKB/Swiss-Prot
      B4DU04, O00296, Q5VWJ2, Q9Y4K1
      Conserved Domains (5) summary
      smart00247
      Location:1023 → 1114
      XTALbg; Beta/gamma crystallins
      PHA03247
      Location:43 → 455
      PHA03247; large tegument protein UL36; Provisional
      PRK12323
      Location:45 → 211
      PRK12323; DNA polymerase III subunit gamma/tau
      cd00161
      Location:1589 → 1717
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam00030
      Location:1219 → 1312
      Crystall; Beta/Gamma crystallin

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      106360717..106572017
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418270.1 → XP_047274226.1  beta/gamma crystallin domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      107536848..107748164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354433.1 → XP_054210408.1  beta/gamma crystallin domain-containing protein 1 isoform X1

    2. XM_054354435.1 → XP_054210410.1  beta/gamma crystallin domain-containing protein 1 isoform X3

    3. XM_054354434.1 → XP_054210409.1  beta/gamma crystallin domain-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y4K1.3 GenPept UniProtKB/Swiss-Prot:Q9Y4K1

    Gene LinkOut

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

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