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Protein

Protein transport protein Sec24D

Gene

SEC24D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the COPII coat, that covers ER-derived vesicles involved in transport from the endoplasmic reticulum to the Golgi apparatus. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the Golgi complex.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

ER-Golgi transport, Protein transport, Transport

Enzyme and pathway databases

BioCyciZFISH:ENSG00000150961-MONOMER.
ReactomeiR-HSA-1655829. Regulation of cholesterol biosynthesis by SREBP (SREBF).
R-HSA-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-HSA-2132295. MHC class II antigen presentation.
R-HSA-5694530. Cargo concentration in the ER.
R-HSA-983170. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein transport protein Sec24D
Alternative name(s):
SEC24-related protein D
Gene namesi
Name:SEC24D
Synonyms:KIAA0755
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:10706. SEC24D.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Golgi apparatus, Membrane

Pathology & Biotechi

Involvement in diseasei

Cole-Carpenter syndrome 2 (CLCRP2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:616294
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073658978Q → P in CLCRP2. 1 PublicationCorresponds to variant rs786204846dbSNPEnsembl.1
Natural variantiVAR_0736591015S → F in CLCRP2. 1 PublicationCorresponds to variant rs760670617dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Osteogenesis imperfecta

Organism-specific databases

DisGeNETi9871.
MIMi616294. phenotype.
OpenTargetsiENSG00000150961.
PharmGKBiPA35629.

Polymorphism and mutation databases

BioMutaiSEC24D.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002051571 – 1032Protein transport protein Sec24DAdd BLAST1032

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei266PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO94855.
MaxQBiO94855.
PaxDbiO94855.
PeptideAtlasiO94855.
PRIDEiO94855.

PTM databases

iPTMnetiO94855.
PhosphoSitePlusiO94855.
SwissPalmiO94855.

Expressioni

Tissue specificityi

Ubiquitously expressed, with higher amounts in placenta, pancreas, heart and liver.

Gene expression databases

BgeeiENSG00000150961.
CleanExiHS_SEC24D.
ExpressionAtlasiO94855. baseline and differential.
GenevisibleiO94855. HS.

Organism-specific databases

HPAiHPA041626.
HPA053486.

Interactioni

Subunit structurei

COPII is composed of at least five proteins: the Sec23/24 complex, the Sec13/31 complex and Sar1. Interacts with TMED2 and TMED10. Interacts with CNIH4 (PubMed:24405750).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EWSR1Q018443EBI-748817,EBI-739737
SEC23BQ154375EBI-748817,EBI-742673
SF3B4Q154273EBI-748817,EBI-348469

Protein-protein interaction databases

BioGridi115204. 30 interactors.
IntActiO94855. 13 interactors.
MINTiMINT-1184580.
STRINGi9606.ENSP00000280551.

Structurei

Secondary structure

11032
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi267 – 278Combined sources12
Beta strandi281 – 284Combined sources4
Beta strandi287 – 289Combined sources3
Beta strandi300 – 302Combined sources3
Beta strandi304 – 306Combined sources3
Turni309 – 311Combined sources3
Beta strandi312 – 322Combined sources11
Helixi323 – 329Combined sources7
Beta strandi334 – 337Combined sources4
Turni356 – 358Combined sources3
Turni364 – 366Combined sources3
Beta strandi375 – 377Combined sources3
Helixi378 – 380Combined sources3
Beta strandi382 – 384Combined sources3
Turni386 – 388Combined sources3
Beta strandi391 – 393Combined sources3
Helixi396 – 398Combined sources3
Beta strandi404 – 406Combined sources3
Turni408 – 410Combined sources3
Helixi411 – 413Combined sources3
Helixi415 – 418Combined sources4
Beta strandi420 – 425Combined sources6
Helixi428 – 430Combined sources3
Helixi432 – 434Combined sources3
Beta strandi441 – 447Combined sources7
Helixi450 – 454Combined sources5
Helixi457 – 468Combined sources12
Helixi469 – 471Combined sources3
Beta strandi478 – 480Combined sources3
Beta strandi484 – 498Combined sources15
Beta strandi507 – 511Combined sources5
Beta strandi522 – 527Combined sources6
Turni529 – 532Combined sources4
Helixi533 – 548Combined sources16
Helixi558 – 571Combined sources14
Beta strandi575 – 581Combined sources7
Beta strandi587 – 589Combined sources3
Helixi607 – 611Combined sources5
Beta strandi614 – 616Combined sources3
Helixi617 – 627Combined sources11
Beta strandi630 – 636Combined sources7
Helixi644 – 647Combined sources4
Helixi649 – 653Combined sources5
Beta strandi658 – 660Combined sources3
Helixi666 – 682Combined sources17
Beta strandi685 – 695Combined sources11
Beta strandi699 – 707Combined sources9
Beta strandi711 – 714Combined sources4
Beta strandi716 – 724Combined sources9
Beta strandi727 – 735Combined sources9
Turni739 – 741Combined sources3
Beta strandi742 – 752Combined sources11
Beta strandi758 – 771Combined sources14
Helixi773 – 778Combined sources6
Helixi782 – 796Combined sources15
Turni797 – 799Combined sources3
Helixi802 – 823Combined sources22
Beta strandi832 – 835Combined sources4
Helixi837 – 839Combined sources3
Helixi842 – 851Combined sources10
Helixi853 – 855Combined sources3
Beta strandi858 – 861Combined sources4
Helixi863 – 875Combined sources13
Helixi878 – 885Combined sources8
Beta strandi888 – 891Combined sources4
Beta strandi897 – 899Combined sources3
Helixi910 – 912Combined sources3
Beta strandi918 – 922Combined sources5
Beta strandi924 – 931Combined sources8
Helixi937 – 944Combined sources8
Beta strandi945 – 948Combined sources4
Helixi949 – 951Combined sources3
Helixi966 – 978Combined sources13
Beta strandi986 – 992Combined sources7
Helixi998 – 1001Combined sources4
Helixi1016 – 1029Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EFOX-ray2.70B266-1032[»]
3EG9X-ray3.00B266-1032[»]
5KYUX-ray3.51B266-1032[»]
5KYWX-ray3.20B266-1032[»]
5KYXX-ray3.52B266-1032[»]
5KYYX-ray3.40B266-1032[»]
ProteinModelPortaliO94855.
SMRiO94855.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO94855.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni363 – 388Zinc finger-likeAdd BLAST26

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 293Pro-richAdd BLAST284

Sequence similaritiesi

Belongs to the SEC23/SEC24 family. SEC24 subfamily.Curated

Phylogenomic databases

eggNOGiKOG1985. Eukaryota.
COG5028. LUCA.
GeneTreeiENSGT00590000082962.
HOGENOMiHOG000196365.
HOVERGENiHBG062229.
InParanoidiO94855.
KOiK14007.
OMAiINTDMTL.
OrthoDBiEOG091G0288.
PhylomeDBiO94855.
TreeFamiTF300464.

Family and domain databases

Gene3Di3.40.20.10. 1 hit.
3.40.50.410. 1 hit.
InterProiIPR029006. ADF-H/Gelsolin-like_dom.
IPR007123. Gelsolin-like_dom.
IPR006900. Sec23/24_helical_dom.
IPR006896. Sec23/24_trunk_dom.
IPR012990. Sec23_24_beta_S.
IPR002035. VWF_A.
IPR006895. Znf_Sec23_Sec24.
[Graphical view]
PfamiPF00626. Gelsolin. 1 hit.
PF08033. Sec23_BS. 1 hit.
PF04815. Sec23_helical. 1 hit.
PF04811. Sec23_trunk. 1 hit.
PF04810. zf-Sec23_Sec24. 1 hit.
[Graphical view]
SUPFAMiSSF53300. SSF53300. 1 hit.
SSF81811. SSF81811. 1 hit.
SSF82754. SSF82754. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O94855-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSQQGYVATP PYSQPQPGIG LSPPHYGHYG DPSHTASPTG MMKPAGPLGA
60 70 80 90 100
TATRGMLPPG PPPPGPHQFG QNGAHATGHP PQRFPGPPPV NNVASSHAPY
110 120 130 140 150
QPSAQSSYPG PISTSSVTQL GSQLSAMQIN SYGSGMAPPS QGPPGPLSAT
160 170 180 190 200
SLQTPPRPPQ PSILQPGSQV LPPPPTTLNG PGASPLPLPM YRPDGLSGPP
210 220 230 240 250
PPNAQYQPPP LPGQTLGAGY PPQQANSGPQ MAGAQLSYPG GFPGGPAQMA
260 270 280 290 300
GPPQPQKKLD PDSIPSPIQV IENDRASRGG QVYATNTRGQ IPPLVTTDCM
310 320 330 340 350
IQDQGNASPR FIRCTTYCFP CTSDMAKQAQ IPLAAVIKPF ATIPSNESPL
360 370 380 390 400
YLVNHGESGP VRCNRCKAYM CPFMQFIEGG RRYQCGFCNC VNDVPPFYFQ
410 420 430 440 450
HLDHIGRRLD HYEKPELSLG SYEYVATLDY CRKSKPPNPP AFIFMIDVSY
460 470 480 490 500
SNIKNGLVKL ICEELKTMLE KIPKEEQEET SAIRVGFITY NKVLHFFNVK
510 520 530 540 550
SNLAQPQMMV VTDVGEVFVP LLDGFLVNYQ ESQSVIHNLL DQIPDMFADS
560 570 580 590 600
NENETVFAPV IQAGMEALKA ADCPGKLFIF HSSLPTAEAP GKLKNRDDKK
610 620 630 640 650
LVNTDKEKIL FQPQTNVYDS LAKDCVAHGC SVTLFLFPSQ YVDVASLGLV
660 670 680 690 700
PQLTGGTLYK YNNFQMHLDR QQFLNDLRND IEKKIGFDAI MRVRTSTGFR
710 720 730 740 750
ATDFFGGILM NNTTDVEMAA IDCDKAVTVE FKHDDKLSED SGALIQCAVL
760 770 780 790 800
YTTISGQRRL RIHNLGLNCS SQLADLYKSC ETDALINFFA KSAFKAVLHQ
810 820 830 840 850
PLKVIREILV NQTAHMLACY RKNCASPSAA SQLILPDSMK VLPVYMNCLL
860 870 880 890 900
KNCVLLSRPE ISTDERAYQR QLVMTMGVAD SQLFFYPQLL PIHTLDVKST
910 920 930 940 950
MLPAAVRCSE SRLSEEGIFL LANGLHMFLW LGVSSPPELI QGIFNVPSFA
960 970 980 990 1000
HINTDMTLLP EVGNPYSQQL RMIMGIIQQK RPYSMKLTIV KQREQPEMVF
1010 1020 1030
RQFLVEDKGL YGGSSYVDFL CCVHKEICQL LN
Length:1,032
Mass (Da):113,010
Last modified:November 25, 2008 - v2
Checksum:iB46E566F096F37F0
GO
Isoform 2 (identifier: O94855-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     224-224: Q → QA

Note: No experimental confirmation available.
Show »
Length:1,033
Mass (Da):113,081
Checksum:i4DBA3D9F630F0043
GO

Sequence cautioni

The sequence BAA34475 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti559P → S in AAD28756 (PubMed:10329445).Curated1
Sequence conflicti559P → S in BAA34475 (PubMed:9872452).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04747242M → T.Corresponds to variant rs10029206dbSNPEnsembl.1
Natural variantiVAR_047473193P → L.Corresponds to variant rs6844109dbSNPEnsembl.1
Natural variantiVAR_047474496F → I.Corresponds to variant rs11723368dbSNPEnsembl.1
Natural variantiVAR_073658978Q → P in CLCRP2. 1 PublicationCorresponds to variant rs786204846dbSNPEnsembl.1
Natural variantiVAR_0736591015S → F in CLCRP2. 1 PublicationCorresponds to variant rs760670617dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_035761224Q → QA in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF130464 mRNA. Translation: AAD28756.2.
AB018298 mRNA. Translation: BAA34475.2. Different initiation.
CH471229 Genomic DNA. Translation: EAW73656.1.
BC035761 mRNA. Translation: AAH35761.1.
CCDSiCCDS3710.1. [O94855-1]
RefSeqiNP_001304995.1. NM_001318066.1. [O94855-2]
NP_055637.2. NM_014822.3. [O94855-1]
XP_005263436.1. XM_005263379.2. [O94855-2]
UniGeneiHs.189641.

Genome annotation databases

EnsembliENST00000280551; ENSP00000280551; ENSG00000150961. [O94855-1]
GeneIDi9871.
KEGGihsa:9871.
UCSCiuc003ici.5. human. [O94855-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF130464 mRNA. Translation: AAD28756.2.
AB018298 mRNA. Translation: BAA34475.2. Different initiation.
CH471229 Genomic DNA. Translation: EAW73656.1.
BC035761 mRNA. Translation: AAH35761.1.
CCDSiCCDS3710.1. [O94855-1]
RefSeqiNP_001304995.1. NM_001318066.1. [O94855-2]
NP_055637.2. NM_014822.3. [O94855-1]
XP_005263436.1. XM_005263379.2. [O94855-2]
UniGeneiHs.189641.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EFOX-ray2.70B266-1032[»]
3EG9X-ray3.00B266-1032[»]
5KYUX-ray3.51B266-1032[»]
5KYWX-ray3.20B266-1032[»]
5KYXX-ray3.52B266-1032[»]
5KYYX-ray3.40B266-1032[»]
ProteinModelPortaliO94855.
SMRiO94855.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115204. 30 interactors.
IntActiO94855. 13 interactors.
MINTiMINT-1184580.
STRINGi9606.ENSP00000280551.

PTM databases

iPTMnetiO94855.
PhosphoSitePlusiO94855.
SwissPalmiO94855.

Polymorphism and mutation databases

BioMutaiSEC24D.

Proteomic databases

EPDiO94855.
MaxQBiO94855.
PaxDbiO94855.
PeptideAtlasiO94855.
PRIDEiO94855.

Protocols and materials databases

DNASUi9871.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000280551; ENSP00000280551; ENSG00000150961. [O94855-1]
GeneIDi9871.
KEGGihsa:9871.
UCSCiuc003ici.5. human. [O94855-1]

Organism-specific databases

CTDi9871.
DisGeNETi9871.
GeneCardsiSEC24D.
H-InvDBHIX0004459.
HGNCiHGNC:10706. SEC24D.
HPAiHPA041626.
HPA053486.
MIMi607186. gene.
616294. phenotype.
neXtProtiNX_O94855.
OpenTargetsiENSG00000150961.
PharmGKBiPA35629.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1985. Eukaryota.
COG5028. LUCA.
GeneTreeiENSGT00590000082962.
HOGENOMiHOG000196365.
HOVERGENiHBG062229.
InParanoidiO94855.
KOiK14007.
OMAiINTDMTL.
OrthoDBiEOG091G0288.
PhylomeDBiO94855.
TreeFamiTF300464.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000150961-MONOMER.
ReactomeiR-HSA-1655829. Regulation of cholesterol biosynthesis by SREBP (SREBF).
R-HSA-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-HSA-2132295. MHC class II antigen presentation.
R-HSA-5694530. Cargo concentration in the ER.
R-HSA-983170. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

Miscellaneous databases

ChiTaRSiSEC24D. human.
EvolutionaryTraceiO94855.
GeneWikiiSEC24D.
GenomeRNAii9871.
PROiO94855.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000150961.
CleanExiHS_SEC24D.
ExpressionAtlasiO94855. baseline and differential.
GenevisibleiO94855. HS.

Family and domain databases

Gene3Di3.40.20.10. 1 hit.
3.40.50.410. 1 hit.
InterProiIPR029006. ADF-H/Gelsolin-like_dom.
IPR007123. Gelsolin-like_dom.
IPR006900. Sec23/24_helical_dom.
IPR006896. Sec23/24_trunk_dom.
IPR012990. Sec23_24_beta_S.
IPR002035. VWF_A.
IPR006895. Znf_Sec23_Sec24.
[Graphical view]
PfamiPF00626. Gelsolin. 1 hit.
PF08033. Sec23_BS. 1 hit.
PF04815. Sec23_helical. 1 hit.
PF04811. Sec23_trunk. 1 hit.
PF04810. zf-Sec23_Sec24. 1 hit.
[Graphical view]
SUPFAMiSSF53300. SSF53300. 1 hit.
SSF81811. SSF81811. 1 hit.
SSF82754. SSF82754. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSC24D_HUMAN
AccessioniPrimary (citable) accession number: O94855
Secondary accession number(s): Q8IYI7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: November 25, 2008
Last modified: November 30, 2016
This is version 146 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.