Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	22984
Gene name	Programmed cell death 11
Gene symbol	PDCD11
Synonyms (NCBI Gene)	ALG-4ALG4NFBPRRP5
Chromosome	10
Chromosome location	10q24.33
Summary	PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[

185

Show/Hide all (185)

miRTarBase ID	miRNA	Experiments	Reference
MIRT027547	hsa-miR-98-5p	Microarray	19088304
MIRT032267	hsa-let-7b-5p	Proteomics	18668040
MIRT032267	hsa-let-7b-5p	CLASH	23622248
MIRT051587	hsa-let-7e-5p	CLASH	23622248
MIRT050784	hsa-miR-17-3p	CLASH	23622248
MIRT040145	hsa-miR-615-3p	CLASH	23622248
MIRT038273	hsa-miR-361-3p	CLASH	23622248
MIRT036204	hsa-miR-320b	CLASH	23622248
MIRT052845	hsa-miR-4286	CLASH	23622248
MIRT655317	hsa-miR-548c-3p	HITS-CLIP	23824327
MIRT655316	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT655315	hsa-miR-6873-5p	HITS-CLIP	23824327
MIRT655314	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT655313	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT655312	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT655317	hsa-miR-548c-3p	HITS-CLIP	23824327
MIRT655316	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT655315	hsa-miR-6873-5p	HITS-CLIP	23824327
MIRT655314	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT655313	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT655312	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT1219185	hsa-let-7a	CLIP-seq
MIRT1219186	hsa-let-7b	CLIP-seq
MIRT1219187	hsa-let-7c	CLIP-seq
MIRT1219188	hsa-let-7d	CLIP-seq
MIRT1219189	hsa-let-7e	CLIP-seq
MIRT1219190	hsa-let-7f	CLIP-seq
MIRT1219191	hsa-let-7g	CLIP-seq
MIRT1219192	hsa-let-7i	CLIP-seq
MIRT1219193	hsa-miR-1200	CLIP-seq
MIRT1219194	hsa-miR-1252	CLIP-seq
MIRT1219195	hsa-miR-132	CLIP-seq
MIRT1219196	hsa-miR-194	CLIP-seq
MIRT1219197	hsa-miR-202	CLIP-seq
MIRT1219198	hsa-miR-212	CLIP-seq
MIRT1219199	hsa-miR-2467-5p	CLIP-seq
MIRT1219200	hsa-miR-3121-3p	CLIP-seq
MIRT1219201	hsa-miR-3188	CLIP-seq
MIRT1219202	hsa-miR-3929	CLIP-seq
MIRT1219203	hsa-miR-3975	CLIP-seq
MIRT1219204	hsa-miR-4316	CLIP-seq
MIRT1219205	hsa-miR-4324	CLIP-seq
MIRT1219206	hsa-miR-4328	CLIP-seq
MIRT1219207	hsa-miR-4419b	CLIP-seq
MIRT1219208	hsa-miR-4458	CLIP-seq
MIRT1219209	hsa-miR-4478	CLIP-seq
MIRT1219210	hsa-miR-4500	CLIP-seq
MIRT1219211	hsa-miR-4649-3p	CLIP-seq
MIRT1219212	hsa-miR-485-5p	CLIP-seq
MIRT1219213	hsa-miR-544b	CLIP-seq
MIRT1219214	hsa-miR-98	CLIP-seq
MIRT2063378	hsa-miR-1207-3p	CLIP-seq
MIRT1219194	hsa-miR-1252	CLIP-seq
MIRT2063379	hsa-miR-1269	CLIP-seq
MIRT2063380	hsa-miR-1269b	CLIP-seq
MIRT2063381	hsa-miR-1288	CLIP-seq
MIRT2063382	hsa-miR-1289	CLIP-seq
MIRT2063383	hsa-miR-185	CLIP-seq
MIRT2063384	hsa-miR-2277-3p	CLIP-seq
MIRT1219199	hsa-miR-2467-5p	CLIP-seq
MIRT2063385	hsa-miR-2861	CLIP-seq
MIRT1219201	hsa-miR-3188	CLIP-seq
MIRT2063386	hsa-miR-3192	CLIP-seq
MIRT2063387	hsa-miR-331-5p	CLIP-seq
MIRT2063388	hsa-miR-3660	CLIP-seq
MIRT2063389	hsa-miR-370	CLIP-seq
MIRT2063390	hsa-miR-378	CLIP-seq
MIRT2063391	hsa-miR-378b	CLIP-seq
MIRT2063392	hsa-miR-378c	CLIP-seq
MIRT2063393	hsa-miR-378d	CLIP-seq
MIRT2063394	hsa-miR-378e	CLIP-seq
MIRT2063395	hsa-miR-378f	CLIP-seq
MIRT2063396	hsa-miR-378h	CLIP-seq
MIRT2063397	hsa-miR-378i	CLIP-seq
MIRT1219202	hsa-miR-3929	CLIP-seq
MIRT1219203	hsa-miR-3975	CLIP-seq
MIRT2063398	hsa-miR-422a	CLIP-seq
MIRT2063399	hsa-miR-4267	CLIP-seq
MIRT2063400	hsa-miR-4306	CLIP-seq
MIRT2063401	hsa-miR-4310	CLIP-seq
MIRT1219204	hsa-miR-4316	CLIP-seq
MIRT1219207	hsa-miR-4419b	CLIP-seq
MIRT1219209	hsa-miR-4478	CLIP-seq
MIRT2063402	hsa-miR-4513	CLIP-seq
MIRT2063403	hsa-miR-4515	CLIP-seq
MIRT2063404	hsa-miR-4526	CLIP-seq
MIRT2063405	hsa-miR-4644	CLIP-seq
MIRT1219211	hsa-miR-4649-3p	CLIP-seq
MIRT2063406	hsa-miR-4685-5p	CLIP-seq
MIRT2063407	hsa-miR-4740-5p	CLIP-seq
MIRT2063408	hsa-miR-4763-5p	CLIP-seq
MIRT2063409	hsa-miR-4802-5p	CLIP-seq
MIRT1219212	hsa-miR-485-5p	CLIP-seq
MIRT2063410	hsa-miR-596	CLIP-seq
MIRT2063411	hsa-miR-766	CLIP-seq
MIRT2291846	hsa-miR-2355-5p	CLIP-seq
MIRT2291847	hsa-miR-3651	CLIP-seq
MIRT2063389	hsa-miR-370	CLIP-seq
MIRT2291848	hsa-miR-4726-3p	CLIP-seq
MIRT2456044	hsa-miR-298	CLIP-seq
MIRT2456045	hsa-miR-4436b-3p	CLIP-seq
MIRT2456046	hsa-miR-4509	CLIP-seq
MIRT2456044	hsa-miR-298	CLIP-seq
MIRT2456045	hsa-miR-4436b-3p	CLIP-seq
MIRT2456046	hsa-miR-4509	CLIP-seq
MIRT2589512	hsa-miR-103a	CLIP-seq
MIRT2589513	hsa-miR-107	CLIP-seq
MIRT2589514	hsa-miR-1286	CLIP-seq
MIRT2589515	hsa-miR-140-3p	CLIP-seq
MIRT2589516	hsa-miR-15a	CLIP-seq
MIRT2589517	hsa-miR-15b	CLIP-seq
MIRT2589518	hsa-miR-16	CLIP-seq
MIRT2589519	hsa-miR-1915	CLIP-seq
MIRT2589520	hsa-miR-195	CLIP-seq
MIRT2063384	hsa-miR-2277-3p	CLIP-seq
MIRT2291846	hsa-miR-2355-5p	CLIP-seq
MIRT2456044	hsa-miR-298	CLIP-seq
MIRT1219200	hsa-miR-3121-3p	CLIP-seq
MIRT2589521	hsa-miR-3158-5p	CLIP-seq
MIRT2589522	hsa-miR-3167	CLIP-seq
MIRT2589523	hsa-miR-330-3p	CLIP-seq
MIRT2291847	hsa-miR-3651	CLIP-seq
MIRT2589524	hsa-miR-3679-3p	CLIP-seq
MIRT2589525	hsa-miR-3943	CLIP-seq
MIRT2589526	hsa-miR-424	CLIP-seq
MIRT2063401	hsa-miR-4310	CLIP-seq
MIRT2589527	hsa-miR-4323	CLIP-seq
MIRT2589528	hsa-miR-4700-3p	CLIP-seq
MIRT2589529	hsa-miR-4722-3p	CLIP-seq
MIRT2589530	hsa-miR-4725-5p	CLIP-seq
MIRT2589531	hsa-miR-4732-3p	CLIP-seq
MIRT2589532	hsa-miR-4749-3p	CLIP-seq
MIRT2589533	hsa-miR-4755-3p	CLIP-seq
MIRT2063408	hsa-miR-4763-5p	CLIP-seq
MIRT2589534	hsa-miR-497	CLIP-seq
MIRT2589535	hsa-miR-504	CLIP-seq
MIRT2063410	hsa-miR-596	CLIP-seq
MIRT2589536	hsa-miR-876-5p	CLIP-seq
MIRT1219185	hsa-let-7a	CLIP-seq
MIRT1219186	hsa-let-7b	CLIP-seq
MIRT1219187	hsa-let-7c	CLIP-seq
MIRT1219188	hsa-let-7d	CLIP-seq
MIRT1219189	hsa-let-7e	CLIP-seq
MIRT1219190	hsa-let-7f	CLIP-seq
MIRT1219191	hsa-let-7g	CLIP-seq
MIRT1219192	hsa-let-7i	CLIP-seq
MIRT2589512	hsa-miR-103a	CLIP-seq
MIRT2589513	hsa-miR-107	CLIP-seq
MIRT1219193	hsa-miR-1200	CLIP-seq
MIRT2589514	hsa-miR-1286	CLIP-seq
MIRT1219195	hsa-miR-132	CLIP-seq
MIRT2589515	hsa-miR-140-3p	CLIP-seq
MIRT2589516	hsa-miR-15a	CLIP-seq
MIRT2589517	hsa-miR-15b	CLIP-seq
MIRT2589518	hsa-miR-16	CLIP-seq
MIRT1219196	hsa-miR-194	CLIP-seq
MIRT2589520	hsa-miR-195	CLIP-seq
MIRT1219197	hsa-miR-202	CLIP-seq
MIRT1219198	hsa-miR-212	CLIP-seq
MIRT2063384	hsa-miR-2277-3p	CLIP-seq
MIRT2291846	hsa-miR-2355-5p	CLIP-seq
MIRT2456044	hsa-miR-298	CLIP-seq
MIRT1219200	hsa-miR-3121-3p	CLIP-seq
MIRT2589521	hsa-miR-3158-5p	CLIP-seq
MIRT2589522	hsa-miR-3167	CLIP-seq
MIRT2589523	hsa-miR-330-3p	CLIP-seq
MIRT2291847	hsa-miR-3651	CLIP-seq
MIRT2589524	hsa-miR-3679-3p	CLIP-seq
MIRT2589526	hsa-miR-424	CLIP-seq
MIRT2063401	hsa-miR-4310	CLIP-seq
MIRT1219205	hsa-miR-4324	CLIP-seq
MIRT1219208	hsa-miR-4458	CLIP-seq
MIRT1219210	hsa-miR-4500	CLIP-seq
MIRT2589528	hsa-miR-4700-3p	CLIP-seq
MIRT2589529	hsa-miR-4722-3p	CLIP-seq
MIRT2589530	hsa-miR-4725-5p	CLIP-seq
MIRT2589531	hsa-miR-4732-3p	CLIP-seq
MIRT2589533	hsa-miR-4755-3p	CLIP-seq
MIRT2063408	hsa-miR-4763-5p	CLIP-seq
MIRT2589534	hsa-miR-497	CLIP-seq
MIRT2589535	hsa-miR-504	CLIP-seq
MIRT1219213	hsa-miR-544b	CLIP-seq
MIRT2063410	hsa-miR-596	CLIP-seq
MIRT2589536	hsa-miR-876-5p	CLIP-seq
MIRT1219214	hsa-miR-98	CLIP-seq

Show/Hide all (14)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IBA
GO:0005515	Function	Protein binding	IPI	14624448
GO:0005634	Component	Nucleus	IDA	14624448
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IBA
GO:0005730	Component	Nucleolus	IEA
GO:0005829	Component	Cytosol	IEA
GO:0006364	Process	RRNA processing	IEA
GO:0006396	Process	RNA processing	IEA
GO:0032040	Component	Small-subunit processome	IBA
GO:0051059	Function	NF-kappaB binding	IPI	14624448

MIM	HGNC	e!Ensembl
612333	13408	ENSG00000148843

Q14690

Protein name

Protein RRP5 homolog (NF-kappa-B-binding protein) (NFBP) (Programmed cell death protein 11)

Protein function

Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. ; Involved in the biogenesis of rRNA. {EC

PDB

1WI5

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00575	S1	449 → 522	S1 RNA binding domain	Domain
PF00575	S1	540 → 611	S1 RNA binding domain	Domain
PF00575	S1	726 → 798	S1 RNA binding domain	Domain
PF00575	S1	1032 → 1100	S1 RNA binding domain	Domain
PF05843	Suf	1725 → 1870	Suppressor of forked protein (Suf)	Family

Sequence

MANLEESFPRGGTRKIHKPEKAFQQSVEQDNLFDISTEEGSTKRKKSQKGPAKTKKLKIE
KRESSKSAREKFEILSVESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYT
KKLNEQVTQEQPLKDLLHLPELFSPGMLVRCVVSSLGITDRGKKSVKLSLNPKNVNRVLS
AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLN
CIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNF
LTFFTGVVDFMHLDPKKAGTYFSNQAVRACILCVHPRTRVVHLSLRPIFLQPGRPLTRLS
CQNLGAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCR
IIDYSQMDELALLSLRTSIIEAQYLRYHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLV
PPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVITCYADAK
PGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCE
PSKERMLLSFKLSSDPEPKKEPAGHSQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPHNI
RAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRKPALVSTVEGGQDP
KNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVA
AKVTNVDEEKQRMLLSLRLSDCGLGDLAITSLLLLNQCLEELQGVRSLMSNRDSVLIQTL
AEMTPGMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVD
LLKLEVHVSLHQDLVNRKARKLRKGSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLN
DTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLAVEGPAAKRTMRPTQKDSETVDEDEEVD
PALTVGTIKKHTLSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTT
KLKVGKTVTARVIGGRDMKTFKYLPISHPRFVRTIPELSVRPSELEDGHTALNTHSVSPM
EKIKQYQAGQTVTCFLKKYNVVKKWLEVEIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVG
QALRATVVGPDSSKTLLCLSLTGPHKLEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSI
FHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLRSSRTNPETKSKVEDPEINSIQD
IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTAR
VLRLNHQKNLVELSFLPGDTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNE
KKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAGLSEEDDSLV
DVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLDSLTPALPPLAESSDSE
EDEKPHQATIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSI
LWLQYMAFHLQATEIEKARAVAERALKTISFREEQEKLNVWVALLNLENMYGSQESLTKV
FERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQ
AAASHRVLQRALECLPSKEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSV
YIDMTIKHGSQKDVRDIFERVIHLSLAPKRMKFFFKRYLDYEKQHGTEKDVQAVKAKALE
YVEAKSSVLED

Sequence length

1871

Interactions

View interactions

	Reactome
			Major pathway of rRNA processing in the nucleolus and cytosol

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTERINE FIBROID	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (1)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Neoplasms	Associate	39511334	★★★★★ ★☆☆☆☆ Found in Text Mining only

PDCD11 (programmed cell death 11)