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FERRY3 FERRY endosomal RAB5 effector complex subunit 3 [ Homo sapiens (human) ]

Gene ID: 57102, updated on 27-Nov-2024

Summary

Official Symbol
FERRY3provided by HGNC
Official Full Name
FERRY endosomal RAB5 effector complex subunit 3provided by HGNC
Primary source
HGNC:HGNC:1184
See related
Ensembl:ENSG00000047621 MIM:616082; AllianceGenome:HGNC:1184
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Fy-3; MRT66; C12orf4
Summary
This gene is highly conserved from nematodes to humans. In rat, the orthologous gene encodes a cytoplasmic protein that is involved in mast cell degranulation. The human gene has been implicated in autosomal recessive intellectual disability. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in brain (RPKM 4.7), thyroid (RPKM 4.4) and 25 other tissues See more
Orthologs
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Genomic context

See FERRY3 in Genome Data Viewer
Location:
12p13.32
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (4487735..4538469, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (4494524..4545256, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (4596901..4647635, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12719 Neighboring gene fibroblast growth factor 23 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4549412-4550163 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4550164-4550914 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4550915-4551665 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4559670-4560372 Neighboring gene fibroblast growth factor 6 Neighboring gene Sharpr-MPRA regulatory region 2870 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4618390-4619024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5825 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:4647270-4647879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:4647880-4648488 Neighboring gene RAD51 associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 10040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5826 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 4 Neighboring gene coiled-coil domain containing 181 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Intellectual disability, autosomal recessive 66
MedGen: C4748732 OMIM: 618221 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Common genetic variants associate with serum phosphorus concentration.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ21158, FLJ23899

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in regulation of mast cell degranulation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of mast cell degranulation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
part_of protein-containing complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
ferry endosomal RAB5 effector complex subunit 3
Names
protein C12orf4

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.

Genomic

  1. NG_051648.1 RefSeqGene

    Range
    5040..55774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304811.2NP_001291740.1  ferry endosomal RAB5 effector complex subunit 3 isoform a

    See identical proteins and their annotated locations for NP_001291740.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AK074479, AL834377, BM556376, DA195770, R59546
    Consensus CDS
    CCDS8528.1
    UniProtKB/Swiss-Prot
    D3DUQ8, Q6MZH5, Q9NQ89
    Related
    ENSP00000439996.1, ENST00000545746.5
    Conserved Domains (1) summary
    pfam10154
    Location:41546
    DUF2362; Uncharacterized conserved protein (DUF2362)
  2. NM_001346153.2NP_001333082.1  ferry endosomal RAB5 effector complex subunit 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
    Source sequence(s)
    AC005832, AC008012, AC092826
  3. NM_001346155.2NP_001333084.1  ferry endosomal RAB5 effector complex subunit 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
    Source sequence(s)
    AC005832, AC008012, AC092826
  4. NM_001346156.2NP_001333085.1  ferry endosomal RAB5 effector complex subunit 3 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
    Source sequence(s)
    AC005832, AC008012, AC092826
    Conserved Domains (1) summary
    pfam10154
    Location:1373
    DUF2362; Uncharacterized conserved protein (DUF2362)
  5. NM_001346157.2NP_001333086.1  ferry endosomal RAB5 effector complex subunit 3 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a.
    Source sequence(s)
    AC005832, AC008012, AC092826
    Conserved Domains (1) summary
    pfam10154
    Location:1330
    DUF2362; Uncharacterized conserved protein (DUF2362)
  6. NM_001352962.2NP_001339891.1  ferry endosomal RAB5 effector complex subunit 3 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC005832, AC008012, AC092826
    Conserved Domains (1) summary
    pfam10154
    Location:1262
    DUF2362; Uncharacterized conserved protein (DUF2362)
  7. NM_020374.4NP_065107.1  ferry endosomal RAB5 effector complex subunit 3 isoform a

    See identical proteins and their annotated locations for NP_065107.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AK074479, AL834377, BM556376, R59546
    Consensus CDS
    CCDS8528.1
    UniProtKB/Swiss-Prot
    D3DUQ8, Q6MZH5, Q9NQ89
    Related
    ENSP00000261250.3, ENST00000261250.8
    Conserved Domains (1) summary
    pfam10154
    Location:41546
    DUF2362; Uncharacterized conserved protein (DUF2362)

RNA

  1. NR_144379.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005832, AC008012, AC092826
  2. NR_144380.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks three alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005832, AC008012, AC092826
  3. NR_144382.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) lacks four alternate exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC005832, AC008012, AC092826

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    4487735..4538469 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718992.4XP_006719055.1  ferry endosomal RAB5 effector complex subunit 3 isoform X1

    Conserved Domains (1) summary
    pfam10154
    Location:41410
    DUF2362; Uncharacterized conserved protein (DUF2362)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    4494524..4545256 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372607.1XP_054228582.1  ferry endosomal RAB5 effector complex subunit 3 isoform X1