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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

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