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CACFD1 calcium channel flower domain containing 1 [ Homo sapiens (human) ]

Gene ID: 11094, updated on 2-Nov-2024

Summary

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Official Symbol
CACFD1provided by HGNC
Official Full Name
calcium channel flower domain containing 1provided by HGNC
Primary source
HGNC:HGNC:1365
See related
Ensembl:ENSG00000160325 MIM:613104; AllianceGenome:HGNC:1365
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
C9orf7; FLOWER; D9S2135
Summary
Predicted to be involved in vesicle-mediated transport. Predicted to be located in several cellular components, including Golgi apparatus; cytoplasmic vesicle; and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in stomach (RPKM 8.2), colon (RPKM 7.0) and 25 other tissues See more
Orthologs
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Genomic context

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See CACFD1 in Genome Data Viewer
Location:
9q34.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133459978..133470848)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145674420..145685255)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136325100..136335970)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene surfeit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20456 Neighboring gene serine/threonine kinase like domain containing 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:136257045-136257682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136265498-136266135 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136267839-136268006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136269742-136270242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29238 Neighboring gene REX4 homolog, 3'-5' exonuclease Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29240 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20458 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136295843-136296052 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136321575-136321727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136322178-136323045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136327558-136328114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29242 Neighboring gene uncharacterized LOC124902295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136344231-136344732 Neighboring gene solute carrier family 2 member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136349490-136350005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136350521-136351036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136351037-136351551 Neighboring gene uncharacterized LOC102723855

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. Membrane structure and internalization dynamics of human Flower isoforms hFWE3 and hFWE4 indicate a conserved endocytic role for hFWE4. Rudd JC, et al. J Biol Chem, 2023 Aug. PMID 37348560, Free PMC Article
  2. Biomarkers for C9orf7-ALS in Symptomatic and Pre-symptomatic Patients: State-of-the-art in the New Era of Clinical Trials. Querin G, et al. J Neuromuscul Dis, 2022. PMID 34864683, Free PMC Article
  3. A synaptic vesicle-associated Ca2+ channel promotes endocytosis and couples exocytosis to endocytosis. Yao CK, et al. Cell, 2009 Sep 4. PMID 19737521, Free PMC Article
  4. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Yuan X, et al. Am J Hum Genet, 2008 Oct. PMID 18940312, Free PMC Article
  5. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. Lou LQ, et al. J Mol Med (Berl), 2023 Mar. PMID 36629882

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Membrane structure and internalization dynamics of human Flower isoforms hFWE3 and hFWE4 indicate a conserved endocytic role for hFWE4.
    Title: Membrane structure and internalization dynamics of human Flower isoforms hFWE3 and hFWE4 indicate a conserved endocytic role for hFWE4.
  2. Biomarkers for C9orf7-ALS in Symptomatic and Pre-symptomatic Patients: State-of-the-art in the New Era of Clinical Trials.
    Title: Biomarkers for C9orf7-ALS in Symptomatic and Pre-symptomatic Patients: State-of-the-art in the New Era of Clinical Trials.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
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 molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
is_active_in cellular_component ND
No biological Data available
more info
  
located_in early endosome IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in recycling endosome IEA
Inferred from Electronic Annotation
more info
  
located_in synaptic vesicle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
calcium channel flower homolog
Names
calcium channel flower domain-containing protein 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.

mRNA and Protein(s)

  1. NM_001135775.4 → NP_001129247.1  calcium channel flower homolog isoform b

    See identical proteins and their annotated locations for NP_001129247.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an two alternate exons compared to variant 3. The resulting isoform (b) has a shorter and distinct C-terminus, compared to isoform c.
    Source sequence(s)
    AA436195, AK075416, AL593848, DB165724
    Consensus CDS
    CCDS48051.1
    UniProtKB/Swiss-Prot
    Q9UGQ2
    Related
    ENSP00000291722.7, ENST00000291722.11
    Conserved Domains (1) summary
    cl10918
    Location:35 → 101
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  2. NM_001242369.2 → NP_001229298.1  calcium channel flower homolog isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AA436195, AK296343, AL593848, BC030558, DB165724
    Consensus CDS
    CCDS56591.1
    UniProtKB/Swiss-Prot
    Q9UGQ2
    Related
    ENSP00000440832.1, ENST00000540581.5
    Conserved Domains (1) summary
    smart01077
    Location:35 → 143
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  3. NM_001242370.2 → NP_001229299.1  calcium channel flower homolog isoform d

    See identical proteins and their annotated locations for NP_001229299.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform c.
    Source sequence(s)
    AA436195, AK074852, AK298820, AL593848, DB165724
    Consensus CDS
    CCDS56592.1
    UniProtKB/Swiss-Prot
    Q9UGQ2
    Related
    ENSP00000444328.1, ENST00000542192.5
    Conserved Domains (1) summary
    cl10918
    Location:35 → 101
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  4. NM_017586.5 → NP_060056.1  calcium channel flower homolog isoform a

    See identical proteins and their annotated locations for NP_060056.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an alternate exon compared to variant 3. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform c.
    Source sequence(s)
    AA436195, AL593848, BC030558, DB165724
    Consensus CDS
    CCDS6974.1
    UniProtKB/Swiss-Prot
    B7Z3T8, B7Z5E1, F5GXX4, Q5SXD4, Q8NBM6, Q9UGQ2
    UniProtKB/TrEMBL
    B7Z969
    Related
    ENSP00000317121.4, ENST00000316948.9
    Conserved Domains (1) summary
    smart01077
    Location:35 → 143
    Cg6151-P; Uncharacterized conserved protein CG6151-P

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    133459978..133470848
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518181.3 → XP_011516483.1  calcium channel flower homolog isoform X1

    See identical proteins and their annotated locations for XP_011516483.1

    Conserved Domains (1) summary
    smart01077
    Location:14 → 115
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  2. XM_011518185.3 → XP_011516487.1  calcium channel flower homolog isoform X4

    See identical proteins and their annotated locations for XP_011516487.1

    UniProtKB/TrEMBL
    B7Z969
    Conserved Domains (1) summary
    smart01077
    Location:14 → 115
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  3. XM_024447398.2 → XP_024303166.1  calcium channel flower homolog isoform X2

    Conserved Domains (1) summary
    smart01077
    Location:1 → 80
    Cg6151-P; Uncharacterized conserved protein CG6151-P

  4. XM_011518184.2 → XP_011516486.1  calcium channel flower homolog isoform X3

    See identical proteins and their annotated locations for XP_011516486.1

    Conserved Domains (1) summary
    cl10918
    Location:14 → 73
    Cg6151-P; Uncharacterized conserved protein CG6151-P

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646201.1 Reference GRCh38.p14 PATCHES

    Range
    286072..296942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331571.1 → XP_054187546.1  calcium channel flower homolog isoform X1

  2. XM_054331574.1 → XP_054187549.1  calcium channel flower homolog isoform X4

  3. XM_054331572.1 → XP_054187547.1  calcium channel flower homolog isoform X2

  4. XM_054331573.1 → XP_054187548.1  calcium channel flower homolog isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145674420..145685255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361867.1 → XP_054217842.1  calcium channel flower homolog isoform X5

  2. XM_054361865.1 → XP_054217840.1  calcium channel flower homolog isoform X1

  3. XM_054361869.1 → XP_054217844.1  calcium channel flower homolog isoform X4

  4. XM_054361866.1 → XP_054217841.1  calcium channel flower homolog isoform X2

  5. XM_054361868.1 → XP_054217843.1  calcium channel flower homolog isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UGQ2.1 GenPept UniProtKB/Swiss-Prot:Q9UGQ2

Gene LinkOut

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

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