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

Gene ID: 202, updated on 2-Nov-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, Nov 2024]
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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See CRYBG1 in Genome Data Viewer
Location:
6q21
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (106360717..106572017)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107536848..107748164)
RS_2024_09 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 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. Loss of heterozygosity for loci on the long arm of chromosome 6 in human malignant melanoma. Millikin D, et al. Cancer Res, 1991 Oct 15. PMID 1680551
  2. AIM1, a novel non-lens member of the betagamma-crystallin superfamily, is associated with the control of tumorigenicity in human malignant melanoma. Ray ME, et al. Proc Natl Acad Sci U S A, 1997 Apr 1. PMID 9096375, Free PMC Article
  3. Stability, homodimerization, and calcium-binding properties of a single, variant betagamma-crystallin domain of the protein absent in melanoma 1 (AIM1). Rajini B, et al. Biochemistry, 2003 Apr 22. PMID 12693952
  4. 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
  5. 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

See all (40) 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/Swiss-Prot
    A0A0J9YWL0, B4DU04, O00296, Q5VWJ2, Q9Y4K1
    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
    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_2024_08

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
Q9Y4K1.4 GenPept UniProtKB/Swiss-Prot:Q9Y4K1

Gene LinkOut

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