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Aliases for SEC24D Gene

Aliases for SEC24D Gene

  • SEC24 Homolog D, COPII Coat Complex Component 2 3 5
  • SEC24-Related Protein D 3 4
  • SEC24 (S. Cerevisiae) Related Gene Family, Member D 2
  • SEC24 Family, Member D (S. Cerevisiae) 2
  • SEC24 Related Gene Family, Member D 3
  • Protein Transport Protein Sec24D 3
  • SEC24 Family Member D 2
  • KIAA0755 4
  • CLCRP2 3

External Ids for SEC24D Gene

Previous GeneCards Identifiers for SEC24D Gene

  • GC04M120402
  • GC04M119924
  • GC04M120037
  • GC04M120102
  • GC04M120001
  • GC04M119643
  • GC04M115365

Summaries for SEC24D Gene

Entrez Gene Summary for SEC24D Gene

  • The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for SEC24D Gene

SEC24D (SEC24 Homolog D, COPII Coat Complex Component) is a Protein Coding gene. Diseases associated with SEC24D include Cole-Carpenter Syndrome 2 and Cole-Carpenter Syndrome. Among its related pathways are Metabolism of proteins and Transport to the Golgi and subsequent modification. An important paralog of this gene is SEC24C.

UniProtKB/Swiss-Prot for SEC24D Gene

  • Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules for their transport to the Golgi complex (PubMed:17499046, PubMed:20427317, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24C may have a different specificity compared to SEC24A and SEC24B (PubMed:17499046, PubMed:20427317, PubMed:18843296). May more specifically package GPI-anchored proteins through the cargo receptor TMED10 (PubMed:20427317). May also be specific for IxM motif-containing cargos like the SNAREs GOSR2 and STX5 (PubMed:18843296).

Gene Wiki entry for SEC24D Gene

Additional gene information for SEC24D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEC24D Gene

Genomics for SEC24D Gene

GeneHancer (GH) Regulatory Elements for SEC24D Gene

Promoters and enhancers for SEC24D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I118833 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.8 +3.3 3282 4 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B SEC24D METTL14 SNHG8 GC04P118810
GH04I118888 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 11.6 -51.1 -51118 2.8 SIN3A ZNF2 ZNF213 ZNF143 KLF7 KLF13 SP3 REST ATF4 ZNF610 SYNPO2 METTL14 SEC24D SNHG8 LOC105377393 GC04M118904
GH04I118275 Promoter/Enhancer 1.8 Ensembl ENCODE 9.9 +559.2 559182 7.7 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SNHG8 SNORA24 METTL14 CICP16 LOC729218 SEC24D FKBP4P1 PRSS12
GH04I118765 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.9 +73.0 72965 0.7 JUN TEAD4 TAL1 FEZF1 FOSL1 TCF12 ZNF366 POLR2A NCOR1 SCRT2 SEC24D METTL14 CEP170P1 GC04P118810
GH04I118917 Enhancer 0.9 Ensembl ENCODE dbSUPER 11.3 -80.0 -79952 1.5 PRDM6 JUND JUN ZNF547 FOS PRDM1 SEC24D GC04M118904 LOC105377393 SYNPO2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SEC24D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEC24D gene promoter:

Genomic Locations for SEC24D Gene

Genomic Locations for SEC24D Gene
chr4:118,722,823-118,838,683
(GRCh38/hg38)
Size:
115,861 bases
Orientation:
Minus strand
chr4:119,643,978-119,759,838
(GRCh37/hg19)

Genomic View for SEC24D Gene

Genes around SEC24D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEC24D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEC24D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEC24D Gene

Proteins for SEC24D Gene

  • Protein details for SEC24D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94855-SC24D_HUMAN
    Recommended name:
    Protein transport protein Sec24D
    Protein Accession:
    O94855
    Secondary Accessions:
    • Q8IYI7

    Protein attributes for SEC24D Gene

    Size:
    1032 amino acids
    Molecular mass:
    113010 Da
    Quaternary structure:
    • COPII is composed of at least five proteins: the Sec23/24 complex, the Sec13/31 complex and Sar1 (PubMed:17499046, PubMed:27551091). Interacts with TMED2 and TMED10 (PubMed:20427317). Interacts with CNIH4 (PubMed:24405750). Interacts with GOSR2 (via IxM motif) and STX5 (via IxM motif); recruits GOSR2 and STX5 into COPII-coated vesicles (PubMed:18843296).
    SequenceCaution:
    • Sequence=BAA34475.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SEC24D Gene

    Alternative splice isoforms for SEC24D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEC24D Gene

Post-translational modifications for SEC24D Gene

  • Ubiquitination at isoforms=2795
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEC24D Gene

Domains & Families for SEC24D Gene

Gene Families for SEC24D Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

O94855

UniProtKB/Swiss-Prot:

SC24D_HUMAN :
  • Belongs to the SEC23/SEC24 family. SEC24 subfamily.
Family:
  • Belongs to the SEC23/SEC24 family. SEC24 subfamily.
genes like me logo Genes that share domains with SEC24D: view

Function for SEC24D Gene

Molecular function for SEC24D Gene

GENATLAS Biochemistry:
SEC24 (S. cerevisiae) related gene family, member D
UniProtKB/Swiss-Prot Function:
Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules for their transport to the Golgi complex (PubMed:17499046, PubMed:20427317, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24C may have a different specificity compared to SEC24A and SEC24B (PubMed:17499046, PubMed:20427317, PubMed:18843296). May more specifically package GPI-anchored proteins through the cargo receptor TMED10 (PubMed:20427317). May also be specific for IxM motif-containing cargos like the SNAREs GOSR2 and STX5 (PubMed:18843296).

Phenotypes From GWAS Catalog for SEC24D Gene

Gene Ontology (GO) - Molecular Function for SEC24D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IPI 18843296
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IDA,IEA 18843296
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SEC24D: view
genes like me logo Genes that share phenotypes with SEC24D: view

Human Phenotype Ontology for SEC24D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEC24D Gene

MGI Knock Outs for SEC24D:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEC24D Gene

Localization for SEC24D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEC24D Gene

Cytoplasmic vesicle, COPII-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm, cytosol.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEC24D gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 5
golgi apparatus 3
nucleus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SEC24D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SEC24D: view

Pathways & Interactions for SEC24D Gene

genes like me logo Genes that share pathways with SEC24D: view

Gene Ontology (GO) - Biological Process for SEC24D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I TAS --
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport TAS,IEA --
genes like me logo Genes that share ontologies with SEC24D: view

No data available for SIGNOR curated interactions for SEC24D Gene

Drugs & Compounds for SEC24D Gene

No Compound Related Data Available

Transcripts for SEC24D Gene

Unigene Clusters for SEC24D Gene

SEC24 family, member D (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEC24D Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4:

ExUns: 24 ^ 25 ^ 26 ^ 27 ^ 28
SP1: -
SP2: -
SP3:
SP4:

Relevant External Links for SEC24D Gene

GeneLoc Exon Structure for
SEC24D
ECgene alternative splicing isoforms for
SEC24D

Expression for SEC24D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEC24D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SEC24D Gene

This gene is overexpressed in Bone marrow stromal cell (15.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SEC24D Gene



Protein tissue co-expression partners for SEC24D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SEC24D Gene:

SEC24D

SOURCE GeneReport for Unigene cluster for SEC24D Gene:

Hs.189641

mRNA Expression by UniProt/SwissProt for SEC24D Gene:

O94855-SC24D_HUMAN
Tissue specificity: Ubiquitously expressed, with higher amounts in placenta, pancreas, heart and liver.

Evidence on tissue expression from TISSUES for SEC24D Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Pancreas(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEC24D Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • skull
  • tongue
  • tooth
  • vocal cord
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
  • placenta
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SEC24D: view

No data available for mRNA differential expression in normal tissues for SEC24D Gene

Orthologs for SEC24D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SEC24D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEC24D 33
  • 97.47 (n)
dog
(Canis familiaris)
Mammalia SEC24D 33 34
  • 90.36 (n)
cow
(Bos Taurus)
Mammalia SEC24D 33 34
  • 87.14 (n)
mouse
(Mus musculus)
Mammalia Sec24d 33 16 34
  • 83.72 (n)
rat
(Rattus norvegicus)
Mammalia Sec24d 33
  • 83.56 (n)
oppossum
(Monodelphis domestica)
Mammalia SEC24D 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEC24D 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEC24D 33 34
  • 74.63 (n)
lizard
(Anolis carolinensis)
Reptilia SEC24D 34
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sec24d 33
  • 69.61 (n)
zebrafish
(Danio rerio)
Actinopterygii sec24d 33 34
  • 66.24 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10576 33
fruit fly
(Drosophila melanogaster)
Insecta CG10882 35
  • 48 (a)
gho 34
  • 39 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sec-24.1 35 34
  • 40 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SFB2 34
  • 24 (a)
ManyToMany
SEC24 34
  • 23 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9094 34
  • 52 (a)
OneToMany
Species where no ortholog for SEC24D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SEC24D Gene

ENSEMBL:
Gene Tree for SEC24D (if available)
TreeFam:
Gene Tree for SEC24D (if available)

Paralogs for SEC24D Gene

Paralogs for SEC24D Gene

(3) SIMAP similar genes for SEC24D Gene using alignment to 9 proteins:

genes like me logo Genes that share paralogs with SEC24D: view

Variants for SEC24D Gene

Sequence variations from dbSNP and Humsavar for SEC24D Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs730882211 likely-pathogenic, Intellectual disability, Seizures 118,815,132(-) C/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs760670617 pathogenic, Cole-Carpenter syndrome 2, Cole-Carpenter syndrome 2 (CLCRP2) [MIM:616294] 118,723,570(-) G/A/C coding_sequence_variant, missense_variant
rs786204845 pathogenic, Cole-Carpenter syndrome 2 118,815,511(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, stop_gained
rs786204846 pathogenic, Cole-Carpenter syndrome 2, Cole-Carpenter syndrome 2 (CLCRP2) [MIM:616294] 118,728,586(-) T/G coding_sequence_variant, missense_variant
rs117971741 likely-benign, not provided 118,768,317(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SEC24D Gene

Variant ID Type Subtype PubMed ID
esv2759279 CNV gain 17122850
esv3601954 CNV loss 21293372
nsv516777 CNV gain 19592680
nsv519017 CNV loss 19592680

Variation tolerance for SEC24D Gene

Residual Variation Intolerance Score: 68.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.08; 60.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEC24D Gene

Human Gene Mutation Database (HGMD)
SEC24D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEC24D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEC24D Gene

Disorders for SEC24D Gene

MalaCards: The human disease database

(6) MalaCards diseases for SEC24D Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cole-carpenter syndrome 2
  • clcrp2
cole-carpenter syndrome
  • bone fragility with craniosynostosis, ocular proptosis, hydrocephalus, and distinctive facial features
carpenter syndrome 2
  • crpt2
brittle cornea syndrome 2
  • bcs2
hyperekplexia
  • congenital stiff man syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SC24D_HUMAN
  • Cole-Carpenter syndrome 2 (CLCRP2) [MIM:616294]: A form of Cole-Carpenter syndrome, a disorder characterized by features of osteogenesis imperfecta such as bone deformities and severe bone fragility with frequent fractures, in association with craniosynostosis, ocular proptosis, hydrocephalus, growth failure and distinctive facial features. Craniofacial findings include marked frontal bossing, midface hypoplasia, and micrognathia. Despite the craniosynostosis and hydrocephalus, intellectual development is normal. CLCRP2 inheritance is autosomal recessive. {ECO:0000269 PubMed:25683121}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SEC24D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEC24D: view

No data available for Genatlas for SEC24D Gene

Publications for SEC24D Gene

  1. Selective export of human GPI-anchored proteins from the endoplasmic reticulum. (PMID: 20427317) Bonnon C … Hauri HP (Journal of cell science 2010) 3 4 22 58
  2. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  3. Mutations in SEC24D, encoding a component of the COPII machinery, cause a syndromic form of osteogenesis imperfecta. (PMID: 25683121) Garbes L … Netzer C (American journal of human genetics 2015) 3 4 58
  4. CNIH4 interacts with newly synthesized GPCR and controls their export from the endoplasmic reticulum. (PMID: 24405750) Sauvageau E … Bouvier M (Traffic (Copenhagen, Denmark) 2014) 3 4 58
  5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 44 58

Products for SEC24D Gene

Sources for SEC24D Gene

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