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    RCAN3 RCAN family member 3 [ Homo sapiens (human) ]

    Gene ID: 11123, updated on 5-Mar-2024

    Summary

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    Official Symbol
    RCAN3provided by HGNC
    Official Full Name
    RCAN family member 3provided by HGNC
    Primary source
    HGNC:HGNC:3042
    See related
    Ensembl:ENSG00000117602 MIM:605860; AllianceGenome:HGNC:3042
    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
    RCN3; MCIP3; hRCN3; DSCR1L2
    Summary
    Enables phosphatase binding activity and troponin I binding activity. Predicted to be involved in calcium-mediated signaling. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in prostate (RPKM 18.2), lymph node (RPKM 9.0) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p36.11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (24502344..24541040)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24340730..24379427)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (24828834..24867530)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene GRHL3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 432 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24648587-24649104 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:24649105-24649620 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:24661406-24662028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664014-24664642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664643-24665269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24669049-24669863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 396 Neighboring gene grainyhead like transcription factor 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:24691307-24692506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 398 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24714266-24714492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 399 Neighboring gene sperm tail PG-rich repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 400 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:24745074-24746273 Neighboring gene NIPA like domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24782303-24782815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:24784099-24784600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 402 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24828715-24828887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 433 Neighboring gene MPRA-validated peak119 silencer Neighboring gene RCAN3 antisense RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24860519-24861170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24861821-24862472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24862473-24863122 Neighboring gene Sharpr-MPRA regulatory region 2491 Neighboring gene NCMAP divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24894097-24894598 Neighboring gene NANOG hESC enhancer GRCh37_chr1:24895749-24896251 Neighboring gene ribosomal protein L26 pseudogene 8 Neighboring gene non-compact myelin associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 435 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24981406-24981591 Neighboring gene small nucleolar RNA U13 Neighboring gene serine and arginine repetitive matrix 1

    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. A novel role for an RCAN3-derived peptide as a tumor suppressor in breast cancer. Martínez-Høyer S, et al. Carcinogenesis, 2015 Jul. PMID 25916653
    2. Human RCAN3 gene expression and cell growth in endothelial cells. Canaider S, et al. Int J Mol Med, 2010 Dec. PMID 21042787
    3. Identification and analysis of human RCAN3 (DSCR1L2) mRNA and protein isoforms. Facchin F, et al. Gene, 2008 Jan 15. PMID 18022329
    4. RCAN3, a novel calcineurin inhibitor that down-regulates NFAT-dependent cytokine gene expression. Mulero MC, et al. Biochim Biophys Acta, 2007 Mar. PMID 17270291
    5. The PxIxIT motif of the RCAN3 inhibits angiogenesis and tumor progression in Triple Negative breast cancer in immunocompetent mice. Biçer A, et al. Carcinogenesis, 2022 Sep 19. PMID 35640493

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The PxIxIT motif of the RCAN3 inhibits angiogenesis and tumor progression in Triple Negative breast cancer in immunocompetent mice.
      Title: The PxIxIT motif of the RCAN3 inhibits angiogenesis and tumor progression in Triple Negative breast cancer in immunocompetent mice.
    2. Functional implications of miR-145/RCAN3 axis in the progression of cervical cancer.
      Title: Functional implications of miR-145/RCAN3 axis in the progression of cervical cancer.
    3. The tumor suppressor effect of RCAN3 in breast cancer depends on the interaction with calcineurin.
      Title: A novel role for an RCAN3-derived peptide as a tumor suppressor in breast cancer.
    4. Studies indicate that RCAN3 is composed of a multigene system that includes at least 21 alternative spliced isoforms.
      Title: Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
    5. Data shows RCAN3 inhibits HUVEC proliferation both basally and under VEGF or phorbol 12-myristate 13-acetate-stimulated conditions, however it does not modulate gene expression of the chosen inflammatory genes.
      Title: Human RCAN3 gene expression and cell growth in endothelial cells.
    6. our data have elucidated the molecular and cellular mechanism whereby PGF(2alpha) regulates CXCL8 expression via the FP receptor in endometrial adenocarcinomas and have highlighted RCAN1-4 as a negative regulator of CXCL8 expression
      Title: Prostaglandin F(2alpha)-F-prostanoid receptor regulates CXCL8 expression in endometrial adenocarcinoma cells via the calcium-calcineurin-NFAT pathway.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in apoptosis and immunoregulation-related genes are associated with risk of chronic lymphocytic leukemia.
    8. The interaction between TNNI3 and the new R variants of RCAN3, RCAN3-2,3,5 and RCAN3-2,4,5, is reported.
      Title: Identification and analysis of human RCAN3 (DSCR1L2) mRNA and protein isoforms.
    9. The yeast cotransformation and GST fusion protein assay demonstrated the interaction between this new DSCR1L2 variant and the human cardiac troponin I.
      Title: Proteins encoded by human Down syndrome critical region gene 1-like 2 (DSCR1L2) mRNA and by a novel DSCR1L2 mRNA isoform interact with cardiac troponin I (TNNI3).
    10. human RCAN3, encoded by the RCAN3 (also known as DSCR1L2) gene, interacts physically and functionally with calcineurin
      Title: RCAN3, a novel calcineurin inhibitor that down-regulates NFAT-dependent cytokine gene expression.
    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

    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 RNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables calcium-dependent protein serine/threonine phosphatase regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables troponin I binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    calcipressin-3
    Names
    Down syndrome candidate region 1-like 2
    Down syndrome critical region gene 1-like 2
    down syndrome candidate region 1-like protein 2
    myocyte-enriched calcineurin-interacting protein 3

    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_001251977.2 → NP_001238906.1  calcipressin-3 isoform 1

      See identical proteins and their annotated locations for NP_001238906.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks a segment in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform 1.
      Source sequence(s)
      AI697154, AL034582, BC035854, CX752875, HQ317421
      Consensus CDS
      CCDS254.1
      UniProtKB/Swiss-Prot
      A4GU14, A4LA69, E3VWE2, E5L4P0, E5L4P7, E7ENV1, E7EWD8, G1FI66, G1FLF0, Q5ECL3, Q5TGC6, Q9NUC8, Q9UKA7, Q9UKA8
      Conserved Domains (1) summary
      pfam04847
      Location:58 → 224
      Calcipressin

    2. NM_001251978.1 → NP_001238907.1  calcipressin-3 isoform 1

      See identical proteins and their annotated locations for NP_001238907.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR exon, compared to variant 1. Variants 1-4 encode the same isoform 1.
      Source sequence(s)
      AI697154, AL034582, HQ287726, HQ317423
      Consensus CDS
      CCDS254.1
      UniProtKB/Swiss-Prot
      A4GU14, A4LA69, E3VWE2, E5L4P0, E5L4P7, E7ENV1, E7EWD8, G1FI66, G1FLF0, Q5ECL3, Q5TGC6, Q9NUC8, Q9UKA7, Q9UKA8
      Conserved Domains (1) summary
      pfam04847
      Location:58 → 224
      Calcipressin

    3. NM_001251979.2 → NP_001238908.1  calcipressin-3 isoform 1

      See identical proteins and their annotated locations for NP_001238908.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR exon, compared to variant 1. Variants 1-4 encode the same isoform 1.
      Source sequence(s)
      AI697154, AL034582, BP326714, HQ317421
      Consensus CDS
      CCDS254.1
      UniProtKB/Swiss-Prot
      A4GU14, A4LA69, E3VWE2, E5L4P0, E5L4P7, E7ENV1, E7EWD8, G1FI66, G1FLF0, Q5ECL3, Q5TGC6, Q9NUC8, Q9UKA7, Q9UKA8
      Related
      ENSP00000445401.2, ENST00000538532.6
      Conserved Domains (1) summary
      pfam04847
      Location:58 → 224
      Calcipressin

    4. NM_001251980.1 → NP_001238909.1  calcipressin-3 isoform 2

      See identical proteins and their annotated locations for NP_001238909.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an in-frame segment in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AF176117, AI697154, AL034582, EF431960, HQ317426
      Consensus CDS
      CCDS57979.1
      UniProtKB/Swiss-Prot
      Q9UKA8
      Related
      ENSP00000409540.2, ENST00000425530.3
      Conserved Domains (1) summary
      pfam04847
      Location:58 → 214
      Calcipressin; Calcipressin

    5. NM_001251981.2 → NP_001238910.1  calcipressin-3 isoform 3

      See identical proteins and their annotated locations for NP_001238910.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AI697154, AL034582, BC035854, CT001954
      Consensus CDS
      CCDS57981.1
      UniProtKB/Swiss-Prot
      Q9UKA8
      Related
      ENSP00000414447.3, ENST00000436717.6
      Conserved Domains (1) summary
      cl17169
      Location:66 → 166
      RRM_SF; RNA recognition motif (RRM) superfamily

    6. NM_001251982.1 → NP_001238911.1  calcipressin-3 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an exon in the coding region, which results in a frame-shift, compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI697154, AL034582, EF467309, HQ287726, HQ317426
      Consensus CDS
      CCDS57980.1
      UniProtKB/Swiss-Prot
      Q9UKA8
      Related
      ENSP00000391912.2, ENST00000412742.5
      Conserved Domains (1) summary
      cl17169
      Location:47 → 123
      RRM_SF; RNA recognition motif (RRM) superfamily

    7. NM_001251983.2 → NP_001238912.1  calcipressin-3 isoform 5

      See identical proteins and their annotated locations for NP_001238912.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) lacks an internal exon, which results in a downstream AUG start codon, compared to variant 1. The resulting isoform (5) is shorter at the N-termius, compared to isoform 1.
      Source sequence(s)
      AI697154, AL034582, BC035854, HQ287726
      Consensus CDS
      CCDS72730.1
      UniProtKB/TrEMBL
      H0YF64
      Related
      ENSP00000478174.1, ENST00000616511.4
      Conserved Domains (1) summary
      cl17169
      Location:2 → 99
      RRM_SF; RNA recognition motif (RRM) superfamily

    8. NM_001251984.2 → NP_001238913.1  calcipressin-3 isoform 5

      See identical proteins and their annotated locations for NP_001238913.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR exon and lacks an internal exon, which results in a downstream AUG start codon, compared to variant 1. The resulting isoform (5) is shorter at the N-termius, compared to isoform 1. Variants 8 and 9 encode the same isoform 5.
      Source sequence(s)
      AI697154, AL034582, BP326714, HQ317421, HQ317422
      Consensus CDS
      CCDS72730.1
      UniProtKB/TrEMBL
      H0YF64
      Related
      ENSP00000484519.1, ENST00000618490.4
      Conserved Domains (1) summary
      cl17169
      Location:2 → 99
      RRM_SF; RNA recognition motif (RRM) superfamily

    9. NM_001251985.1 → NP_001238914.1  calcipressin-3 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) lacks two exons in the coding region, which results in a frame-shift, compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI697154, AL034582, AY906854, HQ317426
      Consensus CDS
      CCDS57982.1
      UniProtKB/Swiss-Prot
      Q9UKA8
      Related
      ENSP00000363514.2, ENST00000374393.4
      Conserved Domains (1) summary
      cl17169
      Location:47 → 67
      RRM_SF; RNA recognition motif (RRM) superfamily

    10. NM_013441.4 → NP_038469.1  calcipressin-3 isoform 1

      See identical proteins and their annotated locations for NP_038469.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1-4 encode the same isoform 1.
      Source sequence(s)
      AI697154, AL034582, BC035854, EF431960
      Consensus CDS
      CCDS254.1
      UniProtKB/Swiss-Prot
      A4GU14, A4LA69, E3VWE2, E5L4P0, E5L4P7, E7ENV1, E7EWD8, G1FI66, G1FLF0, Q5ECL3, Q5TGC6, Q9NUC8, Q9UKA7, Q9UKA8
      Related
      ENSP00000363516.3, ENST00000374395.9
      Conserved Domains (1) summary
      pfam04847
      Location:58 → 224
      Calcipressin

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      24502344..24541040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      24340730..24379427
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKA8.1 GenPept UniProtKB/Swiss-Prot:Q9UKA8

    Gene LinkOut

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

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