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Protein

Nucleoporin NDC1

Gene

NDC1

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

Functioni

Component of the nuclear pore complex (NPC), which plays a key role in de novo assembly and insertion of NPC in the nuclear envelope. Required for NPC and nuclear envelope assembly, possibly by forming a link between the nuclear envelope membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane.2 Publications

Miscellaneous

Depletion of NDC1 from HeLa cells interferes with the assembly of phenylalanine-glycine (FG) repeat Nups into nuclear pore complexes.

GO - Molecular functioni

  • structural constituent of nuclear pore Source: UniProtKB

GO - Biological processi

  • mRNA export from nucleus Source: Reactome
  • nuclear pore complex assembly Source: UniProtKB
  • nuclear pore distribution Source: UniProtKB
  • nuclear pore organization Source: GO_Central
  • protein transport Source: UniProtKB
  • spermatogenesis Source: Ensembl
  • synapsis Source: Ensembl
  • viral process Source: Reactome

Keywordsi

Biological processmRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

ReactomeiR-HSA-1169408 ISG15 antiviral mechanism
R-HSA-159227 Transport of the SLBP independent Mature mRNA
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-168271 Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168276 NS1 Mediated Effects on Host Pathways
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-168333 NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-180746 Nuclear import of Rev protein
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-191859 snRNP Assembly
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-3232142 SUMOylation of ubiquitinylation proteins
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly
R-HSA-3371453 Regulation of HSF1-mediated heat shock response
R-HSA-4085377 SUMOylation of SUMOylation proteins
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-6784531 tRNA processing in the nucleus

Protein family/group databases

TCDBi1.I.1.1.3 the eukaryotic nuclear pore complex (e-npc) family

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoporin NDC1
Short name:
hNDC1
Alternative name(s):
Transmembrane protein 48
Gene namesi
Name:NDC1
Synonyms:TMEM48
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000058804.11
HGNCiHGNC:25525 NDC1
MIMi610115 gene
neXtProtiNX_Q9BTX1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 24CytoplasmicSequence analysisAdd BLAST24
Transmembranei25 – 45Helical; Name=1Sequence analysisAdd BLAST21
Topological domaini46 – 68Perinuclear spaceSequence analysisAdd BLAST23
Transmembranei69 – 89Helical; Name=2Sequence analysisAdd BLAST21
Topological domaini90 – 114CytoplasmicSequence analysisAdd BLAST25
Transmembranei115 – 135Helical; Name=3Sequence analysisAdd BLAST21
Topological domaini136 – 165Perinuclear spaceSequence analysisAdd BLAST30
Transmembranei166 – 186Helical; Name=4Sequence analysisAdd BLAST21
Topological domaini187 – 225CytoplasmicSequence analysisAdd BLAST39
Transmembranei226 – 246Helical; Name=5Sequence analysisAdd BLAST21
Topological domaini247 – 272Perinuclear spaceSequence analysisAdd BLAST26
Transmembranei273 – 293Helical; Name=6Sequence analysisAdd BLAST21
Topological domaini294 – 674CytoplasmicSequence analysisAdd BLAST381

Keywords - Cellular componenti

Membrane, Nuclear pore complex, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi55706
OpenTargetsiENSG00000058804
PharmGKBiPA142670764

Polymorphism and mutation databases

BioMutaiNDC1
DMDMi97180263

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002352401 – 674Nucleoporin NDC1Add BLAST674

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei406PhosphoserineCombined sources1
Modified residuei414PhosphothreonineCombined sources1
Modified residuei439PhosphoserineCombined sources1
Modified residuei440PhosphothreonineCombined sources1
Modified residuei445PhosphoserineCombined sources1
Modified residuei449PhosphothreonineCombined sources1
Modified residuei471PhosphoserineCombined sources1
Modified residuei474PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9BTX1
MaxQBiQ9BTX1
PaxDbiQ9BTX1
PeptideAtlasiQ9BTX1
PRIDEiQ9BTX1
ProteomicsDBi79021
79022 [Q9BTX1-2]
79023 [Q9BTX1-3]
79024 [Q9BTX1-4]

PTM databases

iPTMnetiQ9BTX1
PhosphoSitePlusiQ9BTX1
SwissPalmiQ9BTX1

Expressioni

Gene expression databases

BgeeiENSG00000058804 Expressed in 215 organ(s), highest expression level in female gonad
CleanExiHS_TMEM48
GenevisibleiQ9BTX1 HS

Organism-specific databases

HPAiHPA069751
HPA070882

Interactioni

Subunit structurei

Interacts with the NUP35/NUP53 (By similarity). Interacts with AAAS, anchoring it to the nuclear envelope.By similarity1 Publication

Protein-protein interaction databases

BioGridi120831, 54 interactors
IntActiQ9BTX1, 24 interactors
STRINGi9606.ENSP00000360483

Structurei

3D structure databases

ProteinModelPortaliQ9BTX1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDC1 family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4358 Eukaryota
ENOG4110XEC LUCA
GeneTreeiENSGT00390000014590
HOGENOMiHOG000231135
HOVERGENiHBG080133
InParanoidiQ9BTX1
KOiK14315
OMAiHFKLPHA
OrthoDBiEOG091G0MME
PhylomeDBiQ9BTX1
TreeFamiTF324843

Family and domain databases

InterProiView protein in InterPro
IPR019049 Nucleoporin_prot_Ndc1/Nup
PANTHERiPTHR13269 PTHR13269, 1 hit
PfamiView protein in Pfam
PF09531 Ndc1_Nup, 1 hit

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q9BTX1-1) [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
MATAVSRPCA GRSRDILWRV LGWRIVASIV WSVLFLPICT TVFIIFSRID
60 70 80 90 100
LFHPIQWLSD SFSDLYSSYV IFYFLLLSVV IIIISIFNVE FYAVVPSIPC
110 120 130 140 150
SRLALIGKII HPQQLMHSFI HAAMGMVMAW CAAVITQGQY SFLVVPCTGT
160 170 180 190 200
NSFGSPAAQT CLNEYHLFFL LTGAFMGYSY SLLYFVNNMN YLPFPIIQQY
210 220 230 240 250
KFLRFRRSLL LLVKHSCVES LFLVRNFCIL YYFLGYIPKA WISTAMNLHI
260 270 280 290 300
DEQVHRPLDT VSGLLNLSLL YHVWLCGVFL LTTWYVSWIL FKIYATEAHV
310 320 330 340 350
FPVQPPFAEG SDECLPKVLN SNPPPIIKYL ALQDLMLLSQ YSPSRRQEVF
360 370 380 390 400
SLSQPGGHPH NWTAISRECL NLLNGMTQKL ILYQEAAATN GRVSSSYPVE
410 420 430 440 450
PKKLNSPEET AFQTPKSSQM PRPSVPPLVK TSLFSSKLST PDVVSPFGTP
460 470 480 490 500
FGSSVMNRMA GIFDVNTCYG SPQSPQLIRR GPRLWTSASD QQMTEFSNPS
510 520 530 540 550
PSTSISAEGK TMRQPSVIYS WIQNKREQIK NFLSKRVLIM YFFSKHPEAS
560 570 580 590 600
IQAVFSDAQM HIWALEGLSH LVAASFTEDR FGVVQTTLPA ILNTLLTLQE
610 620 630 640 650
AVDKYFKLPH ASSKPPRISG SLVDTSYKTL RFAFRASLKT AIYRITTTFG
660 670
EHLNAVQASA EHQKRLQQFL EFKE
Length:674
Mass (Da):76,305
Last modified:May 16, 2006 - v2
Checksum:i78368FEB232895D9
GO
Isoform 2 (identifier: Q9BTX1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     93-93: Missing.

Note: No experimental confirmation available.
Show »
Length:673
Mass (Da):76,234
Checksum:i27A688260C1B2852
GO
Isoform 3 (identifier: Q9BTX1-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     376-492: Missing.

Note: No experimental confirmation available.
Show »
Length:557
Mass (Da):63,572
Checksum:iC9AC3DCCCF3D5EBE
GO
Isoform 4 (identifier: Q9BTX1-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     509-542: GKTMRQPSVIYSWIQNKREQIKNFLSKRVLIMYF → APRGLHSGCFFRCPNAYLGIRRSVALSSSIIYRG
     543-674: Missing.

Note: No experimental confirmation available.
Show »
Length:542
Mass (Da):61,009
Checksum:i06630F6E487BAC55
GO
Isoform 5 (identifier: Q9BTX1-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     95-135: VPSIPCSRLALIGKIIHPQQLMHSFIHAAMGMVMAWCAAVI → I

Note: No experimental confirmation available.
Show »
Length:634
Mass (Da):71,992
Checksum:iF80C5BBAFEF9C41F
GO
Isoform 6 (identifier: Q9BTX1-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-115: Missing.

Note: No experimental confirmation available.
Show »
Length:559
Mass (Da):63,158
Checksum:iB2DD7D9EE6AF56EA
GO

Sequence cautioni

The sequence BAB14135 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAC03665 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti261V → A in BAG58064 (PubMed:14702039).Curated1
Sequence conflicti476Q → R in BAG58064 (PubMed:14702039).Curated1
Sequence conflicti525K → R in BAG61017 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026388154G → D2 PublicationsCorresponds to variant dbSNP:rs17849721Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0553311 – 115Missing in isoform 6. 1 PublicationAdd BLAST115
Alternative sequenceiVSP_01839693Missing in isoform 2. 1 Publication1
Alternative sequenceiVSP_05533295 – 135VPSIP…CAAVI → I in isoform 5. 1 PublicationAdd BLAST41
Alternative sequenceiVSP_018397376 – 492Missing in isoform 3. 1 PublicationAdd BLAST117
Alternative sequenceiVSP_018398509 – 542GKTMR…LIMYF → APRGLHSGCFFRCPNAYLGI RRSVALSSSIIYRG in isoform 4. CuratedAdd BLAST34
Alternative sequenceiVSP_018399543 – 674Missing in isoform 4. CuratedAdd BLAST132

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141696 mRNA Translation: AAZ73087.1
AK001269 mRNA Translation: BAA91592.1
AK022618 mRNA Translation: BAB14135.1 Different initiation.
AK091439 mRNA Translation: BAC03665.1 Different initiation.
AK298909 mRNA Translation: BAG61017.1
AK295000 mRNA Translation: BAG58064.1
AL354612 mRNA Translation: CAB89725.1
AL354613 mRNA Translation: CAB89726.1
AL049745 Genomic DNA No translation available.
CH471059 Genomic DNA Translation: EAX06731.1
BC003082 mRNA Translation: AAH03082.1
CCDSiCCDS583.1 [Q9BTX1-1]
RefSeqiNP_001162023.1, NM_001168551.1 [Q9BTX1-5]
NP_060557.3, NM_018087.4 [Q9BTX1-1]
UniGeneiHs.476525

Genome annotation databases

EnsembliENST00000371429; ENSP00000360483; ENSG00000058804 [Q9BTX1-1]
GeneIDi55706
KEGGihsa:55706
UCSCiuc001cvs.4 human [Q9BTX1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141696 mRNA Translation: AAZ73087.1
AK001269 mRNA Translation: BAA91592.1
AK022618 mRNA Translation: BAB14135.1 Different initiation.
AK091439 mRNA Translation: BAC03665.1 Different initiation.
AK298909 mRNA Translation: BAG61017.1
AK295000 mRNA Translation: BAG58064.1
AL354612 mRNA Translation: CAB89725.1
AL354613 mRNA Translation: CAB89726.1
AL049745 Genomic DNA No translation available.
CH471059 Genomic DNA Translation: EAX06731.1
BC003082 mRNA Translation: AAH03082.1
CCDSiCCDS583.1 [Q9BTX1-1]
RefSeqiNP_001162023.1, NM_001168551.1 [Q9BTX1-5]
NP_060557.3, NM_018087.4 [Q9BTX1-1]
UniGeneiHs.476525

3D structure databases

ProteinModelPortaliQ9BTX1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120831, 54 interactors
IntActiQ9BTX1, 24 interactors
STRINGi9606.ENSP00000360483

Protein family/group databases

TCDBi1.I.1.1.3 the eukaryotic nuclear pore complex (e-npc) family

PTM databases

iPTMnetiQ9BTX1
PhosphoSitePlusiQ9BTX1
SwissPalmiQ9BTX1

Polymorphism and mutation databases

BioMutaiNDC1
DMDMi97180263

Proteomic databases

EPDiQ9BTX1
MaxQBiQ9BTX1
PaxDbiQ9BTX1
PeptideAtlasiQ9BTX1
PRIDEiQ9BTX1
ProteomicsDBi79021
79022 [Q9BTX1-2]
79023 [Q9BTX1-3]
79024 [Q9BTX1-4]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000371429; ENSP00000360483; ENSG00000058804 [Q9BTX1-1]
GeneIDi55706
KEGGihsa:55706
UCSCiuc001cvs.4 human [Q9BTX1-1]

Organism-specific databases

CTDi55706
DisGeNETi55706
EuPathDBiHostDB:ENSG00000058804.11
GeneCardsiNDC1
H-InvDBiHIX0000603
HGNCiHGNC:25525 NDC1
HPAiHPA069751
HPA070882
MIMi610115 gene
neXtProtiNX_Q9BTX1
OpenTargetsiENSG00000058804
PharmGKBiPA142670764
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4358 Eukaryota
ENOG4110XEC LUCA
GeneTreeiENSGT00390000014590
HOGENOMiHOG000231135
HOVERGENiHBG080133
InParanoidiQ9BTX1
KOiK14315
OMAiHFKLPHA
OrthoDBiEOG091G0MME
PhylomeDBiQ9BTX1
TreeFamiTF324843

Enzyme and pathway databases

ReactomeiR-HSA-1169408 ISG15 antiviral mechanism
R-HSA-159227 Transport of the SLBP independent Mature mRNA
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-168271 Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168276 NS1 Mediated Effects on Host Pathways
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-168333 NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-180746 Nuclear import of Rev protein
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-191859 snRNP Assembly
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-3232142 SUMOylation of ubiquitinylation proteins
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly
R-HSA-3371453 Regulation of HSF1-mediated heat shock response
R-HSA-4085377 SUMOylation of SUMOylation proteins
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-6784531 tRNA processing in the nucleus

Miscellaneous databases

ChiTaRSiNDC1 human
GeneWikiiTMEM48
GenomeRNAii55706
PROiPR:Q9BTX1
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000058804 Expressed in 215 organ(s), highest expression level in female gonad
CleanExiHS_TMEM48
GenevisibleiQ9BTX1 HS

Family and domain databases

InterProiView protein in InterPro
IPR019049 Nucleoporin_prot_Ndc1/Nup
PANTHERiPTHR13269 PTHR13269, 1 hit
PfamiView protein in Pfam
PF09531 Ndc1_Nup, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiNDC1_HUMAN
AccessioniPrimary (citable) accession number: Q9BTX1
Secondary accession number(s): B4DHA3
, B4DQQ5, G3XA81, Q8NB76, Q9H9T6, Q9NSG3, Q9NSG4, Q9NVZ7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 16, 2006
Last modified: November 7, 2018
This is version 136 of the entry and version 2 of the sequence. See 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

Complete proteome, Reference proteome

Documents

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