CleftGeneDB-Search

Gene: Col4a4

Basic information

Tag	Content
Uniprot ID	Q9QZR9; Q149M2; Q64457;
Entrez ID	12829
Genbank protein ID	CAA84530.1; AAD50450.1; AAI17710.1;
Genbank nucleotide ID	NM_007735.2
Ensembl protein ID	ENSMUSP00000084282
Ensembl nucleotide ID	ENSMUSG00000067158
Gene name	Collagen alpha-4(IV) chain
Gene symbol	Col4a4
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type
Developmental stage
Data sources	Homology search
Reference
Functional description	Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.
Sequence	MRCFFRWTKS FVTAPWSLIF ILFTIQYEYG SGKKYGGPCG GRNCSVCQCF PEKGSRGHPG 60 PLGPQGPIGP LGPLGPIGIP GEKGERGDSG SPGPPGEKGD KGPTGVPGFP GVDGVPGHPG 120 PPGPRGKPGV DGYNGSRGDP GYPGERGAPG PGGPPGQPGE NGEKGRSVYI TGGVKGIQGD 180 RGDPGPPGLP GSRGAQGSPG PMGHAGAPGL AGPIGHPGSP GLKGNPATGL KGQRGEPGEV 240 GQRGPPGPTL LVQPPDLSIY KGEKGVKGMP GMIGPPGPPG RKGAPGVGIK GEKGIPGFPG 300 PRGEPGSHGP PGFPGFKGIQ GAAGEPGLFG FLGPKGDLGD RGYPGPPGIL LTPAPPLKGV 360 PGDPGPPGYY GEIGDVGLPG PPGPPGRPGE TCPGMMGPPG PPGVPGPPGF PGEAGVPGRL 420 DCAPGKPGKP GLPGLPGAPG PEGPPGSDVI YCRPGCPGPM GEKGKVGPPG RRGAKGAKGN 480 KGLCTCPPGP MGPPGPPGPP GRQGSKGDLG LPGWHGEKGD PGQPGAEGPP GPPGRPGAMG 540 PPGHKGEKGD MVISRVKGQK GERGLDGPPG FPGPHGQDGG DGRPGERGDP GPRGDHKDAA 600 PGERGLPGLP GPPGRTGPEG PPGLGFPGPP GQRGLPGEPG RPGTRGFDGT KGQKGDSILC 660 NVSYPGKPGL PGLDGPPGLK GFPGPPGAPG MRCPDGQKGQ RGKPGMSGIP GPPGFRGDMG 720 DPGIKGEKGT SPIGPPGPPG SPGKDGQKGI PGDPAFGDPG PPGERGLPGA PGMKGQKGHP 780 GCPGAGGPPG IPGSPGLKGP KGREGSRGFP GIPGSPGHSC ERGAPGIPGQ PGLPGTPGDP 840 GAPGWKGQPG DMGPSGPAGM KGLPGLPGLP GADGLRGPPG IPGPNGEDGL PGLPGLKGLP 900 GLPGFPGFPG ERGKPGPDGE PGRKGEVGEK GWPGLKGDLG ERGAKGDRGL PGDAGEAVTS 960 RKGEPGDAGP PGDGGFSGER GDKGSSGMRG GRGDPGRDGL PGLHRGQPGI DGPPGPPGPP 1020 GPPGSPGLRG VIGFPGFPGD QGDPGSPGPP GFPGDDGARG PKGYKGDPAS QCGPPGPKGE 1080 PGSPGYQGRT GVPGEKGFPG DEGPRGPPGR PGQPGSFGPP GCPGDPGMPG LKGHPGEVGD 1140 PGPRGDAGDF GRPGPAGVKG PLGSPGLNGL HGLKGEKGTK GASGLLEMGP PGPMGMPGQK 1200 GEKGDPGSPG ISPPGLPGEK GFPGPPGRPG PPGPAGAPGR AAKGDIPDPG PPGDRGPPGP 1260 DGPRGVPGPP GSPGNVDLLK GDPGDCGLPG PPGSRGPPGP PGCQGPPGCD GKDGQKGPMG 1320 LPGLPGPPGL PGAPGEKGLP GPPGRKGPVG PPGCRGEPGP PADVDSCPRI PGLPGVPGPR 1380 GPEGAMGEPG RRGLPGPGCK GEPGPDGRRG QDGIPGSPGP PGRKGDTGEA GCPGAPGPPG 1440 PTGDPGPKGF GPGSLSGFLL VLHSQTDQEP ACPVGMPRLW TGYSLLYMEG QEKAHNQDLG 1500 LAGSCLPVFS TLPFAYCNIH QVCHYAQRND RSYWLSSAAP LPMMPLSEEE IRSYISRCAV 1560 CEAPAQAVAV HSQDQSIPPC PRTWRSLWIG YSFLMHTGAG DQGGGQALMS PGSCLEDFRA 1620 APFVECQGRQ GTCHFFANEY SFWLTTVNPD LQFASGPSPD TLKEVQAQRR KISRCQVCMK 1680 HS 1682

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Species	Evidence	Details
1:1 ortholog	COL4A4		A0A452G3N1	Capra hircus	Prediction	More>>
1:1 ortholog	COL4A4	1286	P53420	Homo sapiens	Publication	More>>
1:1 ortholog	Col4a4	12829	Q9QZR9	Mus musculus	Prediction	More>>
1:1 ortholog	COL4A4	459986	H2R630	Pan troglodytes	Prediction	More>>
1:1 ortholog	Col4a4		A0A0G2K742	Rattus norvegicus	Prediction	More>>

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs30245052	p.Thr13Ile	missense variant	-	NC_000067.6:g.82571378G>A	UniProt
rs216312698	p.Ser17Leu	missense variant	-	NC_000067.6:g.82569844G>A	UniProt
rs239510227	p.Pro67Ser	missense variant	-	NC_000067.6:g.82541274G>A	UniProt
rs219272625	p.Leu74Pro	missense variant	-	NC_000067.6:g.82541252A>G	UniProt
rs30245626	p.Pro92Thr	missense variant	-	NC_000067.6:g.82541199G>T	UniProt
rs1134550215	p.Pro92Leu	missense variant	-	NC_000067.6:g.82541198G>A	UniProt
rs254448400	p.Tyr133Phe	missense variant	-	NC_000067.6:g.82539098T>A	UniProt
rs221342590	p.Pro140Leu	missense variant	-	NC_000067.6:g.82539077G>A	UniProt
rs30248726	p.Thr171Ser	missense variant	-	NC_000067.6:g.82535764T>A	UniProt
rs261075164	p.Val174Ile	missense variant	-	NC_000067.6:g.82535755C>T	UniProt
rs1132610872	p.Ile214Thr	missense variant	-	NC_000067.6:g.82531628A>G	UniProt
rs1133392123	p.Asn225Ser	missense variant	-	NC_000067.6:g.82531395T>C	UniProt
rs1132424119	p.Ala227Thr	missense variant	-	NC_000067.6:g.82531390C>T	UniProt
rs225236047	p.Pro310Ser	missense variant	-	NC_000067.6:g.82527552G>A	UniProt
rs1134319499	p.Gly333Ala	missense variant	-	NC_000067.6:g.82525872C>G	UniProt
rs243686281	p.Leu338Pro	missense variant	-	NC_000067.6:g.82525049A>G	UniProt
rs30245934	p.Val466Met	missense variant	-	NC_000067.6:g.82509207C>T	UniProt
rs30246789	p.Lys481Glu	missense variant	-	NC_000067.6:g.82507104T>C	UniProt
rs241713344	p.Asp566Asn	missense variant	-	NC_000067.6:g.82497911C>T	UniProt
rs222074960	p.Pro572Leu	missense variant	-	NC_000067.6:g.82497892G>A	UniProt
rs30249886	p.Pro612Leu	missense variant	-	NC_000067.6:g.82497282G>A	UniProt
rs30249887	p.Glu619Val	missense variant	-	NC_000067.6:g.82497261T>A	UniProt
rs242591176	p.Glu638Asp	missense variant	-	NC_000067.6:g.82497203C>A	UniProt
rs255636452	p.Thr650Met	missense variant	-	NC_000067.6:g.82497168G>A	UniProt
rs226146926	p.Met691Arg	missense variant	-	NC_000067.6:g.82493561A>C	UniProt
rs263572311	p.Gly708Glu	missense variant	-	NC_000067.6:g.82493510C>T	UniProt
rs231018080	p.Met719Val	missense variant	-	NC_000067.6:g.82492652T>C	UniProt
rs1133145634	p.Ile724Asn	missense variant	-	NC_000067.6:g.82492636A>T	UniProt
rs1132607133	p.Glu764Lys	missense variant	-	NC_000067.6:g.82492517C>T	UniProt
rs211799821	p.Pro771Thr	missense variant	-	NC_000067.6:g.82492496G>T	UniProt
rs234255469	p.Ser815Cys	missense variant	-	NC_000067.6:g.82491602G>C	UniProt
rs30245919	p.Arg876Gln	missense variant	-	NC_000067.6:g.82489765C>T	UniProt
rs1133295886	p.Gly877Glu	missense variant	-	NC_000067.6:g.82489762C>T	UniProt
rs224022317	p.Pro878Leu	missense variant	-	NC_000067.6:g.82489759G>A	UniProt
rs246438824	p.Pro878Ser	missense variant	-	NC_000067.6:g.82489760G>A	UniProt
rs257712404	p.Asn885Thr	missense variant	-	NC_000067.6:g.82489738T>G	UniProt
rs234580787	p.Leu899Ile	missense variant	-	NC_000067.6:g.82489152G>T	UniProt
rs263879351	p.Pro915Ser	missense variant	-	NC_000067.6:g.82489104G>A	UniProt
rs243396129	p.Glu979Lys	missense variant	-	NC_000067.6:g.82487518C>T	UniProt
rs215027610	p.Ser986Pro	missense variant	-	NC_000067.6:g.82486650A>G	UniProt
rs30247435	p.Leu1000Pro	missense variant	-	NC_000067.6:g.82486607A>G	UniProt
rs48845860	p.Pro1049Leu	missense variant	-	NC_000067.6:g.82485622G>A	UniProt
rs236056563	p.Ala1069Asp	missense variant	-	NC_000067.6:g.82484447G>T	UniProt
rs235167763	p.Arg1089His	missense variant	-	NC_000067.6:g.82480586C>T	UniProt
rs240674534	p.Val1092Ala	missense variant	-	NC_000067.6:g.82480577A>G	UniProt
rs240796564	p.Val1138Met	missense variant	-	NC_000067.6:g.82479924C>T	UniProt
rs256382071	p.Leu1162Pro	missense variant	-	NC_000067.6:g.82472543A>G	UniProt
rs220146580	p.Pro1223Ser	missense variant	-	NC_000067.6:g.82471201G>A	UniProt
rs232749933	p.Ala1235Thr	missense variant	-	NC_000067.6:g.82471073C>T	UniProt
rs1133906622	p.Arg1255Trp	missense variant	-	NC_000067.6:g.82471013G>A	UniProt
rs229223771	p.Asp1285Glu	missense variant	-	NC_000067.6:g.82469573G>T	UniProt
rs6389257	p.Arg1295Gln	missense variant	-	NC_000067.6:g.82469544C>T	UniProt
rs266181178	p.Arg1391Gln	missense variant	-	NC_000067.6:g.82462071C>T	UniProt
rs218014037	p.Pro1397Leu	missense variant	-	NC_000067.6:g.82462053G>A	UniProt
rs250043260	p.Arg1531Lys	missense variant	-	NC_000067.6:g.82453970C>T	UniProt
rs228470583	p.Ser1553Pro	missense variant	-	NC_000067.6:g.82453905A>G	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0005201	extracellular matrix structural constituent	ISO
GO:0005201	extracellular matrix structural constituent	IBA
GO:0005201	extracellular matrix structural constituent	IPI
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0030198	extracellular matrix organization	IBA
GO:0032836	glomerular basement membrane development	ISO
GO:0032836	glomerular basement membrane development	IMP
GO:0032836	glomerular basement membrane development	IBA
GO:0038063	collagen-activated tyrosine kinase receptor signaling pathway	IBA

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005587	collagen type IV trimer	ISO
GO:0005587	collagen type IV trimer	IBA
GO:0005587	collagen type IV trimer	IDA
GO:0005604	basement membrane	ISS
GO:0005604	basement membrane	ISO
GO:0005604	basement membrane	IDA
GO:0005615	extracellular space	IBA
GO:0031012	extracellular matrix	IBA
GO:0062023	collagen-containing extracellular matrix	HDA

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-1266738	Developmental Biology	IEA
R-MMU-1442490	Collagen degradation	IEA
R-MMU-1474228	Degradation of the extracellular matrix	IEA
R-MMU-1474244	Extracellular matrix organization	IEA
R-MMU-1474290	Collagen formation	IEA
R-MMU-162582	Signal Transduction	IEA
R-MMU-1650814	Collagen biosynthesis and modifying enzymes	IEA
R-MMU-186797	Signaling by PDGF	IEA
R-MMU-2022090	Assembly of collagen fibrils and other multimeric structures	IEA
R-MMU-216083	Integrin cell surface interactions	IEA
R-MMU-2214320	Anchoring fibril formation	IEA
R-MMU-2243919	Crosslinking of collagen fibrils	IEA
R-MMU-3000157	Laminin interactions	IEA
R-MMU-3000171	Non-integrin membrane-ECM interactions	IEA
R-MMU-375165	NCAM signaling for neurite out-growth	IEA
R-MMU-419037	NCAM1 interactions	IEA
R-MMU-422475	Axon guidance	IEA
R-MMU-8948216	Collagen chain trimerization	IEA
R-MMU-9006934	Signaling by Receptor Tyrosine Kinases	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0025	Alternative splicing
KW-0084	Basement membrane
KW-0176	Collagen
KW-1015	Disulfide bond
KW-0272	Extracellular matrix
KW-0325	Glycoprotein
KW-0379	Hydroxylation
KW-1185	Reference proteome
KW-0677	Repeat
KW-0964	Secreted
KW-0732	Signal

Interpro

InterPro ID	InterPro Term
IPR008160	Collagen
IPR001442	Collagen_IV_NC
IPR036954	Collagen_IV_NC_sf
IPR016187	CTDL_fold

PROSITE

PROSITE ID	PROSITE Term
PS51403	NC1_IV

Pfam

Pfam ID	Pfam Term
PF01413	C4
PF01391	Collagen

Gene: Col4a4

Basic information

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-miRNA interaction