PROSITE documentation PDOC50171
Zinc finger matrin-type profile


This C2H2 zinc finger was first identified in the protein Matrin 3 [1]. It is also found in several spliceosome RNA-binding proteins, suggesting a possible role in pre-mRNA binding.

The matrin zinc finger follows the general pattern C-x2-C-x(12,16)-H-x5-H. The spacings are different from the 'classical' DNA-binding C2H2 zinc finger (see <PDOC00028>), nevertheless these two domains are too closely related to be fully separated by a pattern.

Some of the proteins containing this domain are listed below:

  • Matrin 3. May interact with other nuclear matrix proteins to form the internal fibrogranular network.
  • Eukaryotic splicing factor 3A subunits 2 (SAP62/PRP11) and 3 (SAP60/PRP9). These are subunits of the SF3A complex required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. May anchor U2 snRNP to pre-mRNA.
  • U1 small nuclear ribonucleoprotein C. Directly bind pre-mRNA [2].
  • Mammalian nuclear protein NP220. Related to matrin 3.
  • Formin binding protein 21, a spliceosome-associated protein.

We have developed a profile that covers the whole zinc finger with 2 positions upstream, usually aromatic, and 5 positions downstream which could form a positively charge tail important for RNA binding activity.

Last update:

December 2001 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

ZF_MATRIN, PS50171; Zinc finger matrin-type profile  (MATRIX)


1AuthorsMatsushima Y. Matsumura K. Kitagawa Y.
TitleZinc finger-like motif conserved in a family of RNA binding proteins.
SourceBiosci. Biotechnol. Biochem. 61:905-906(1997).
PubMed ID9178570

2AuthorsRossi F. Forne T. Antoine E. Tazi J. Brunel C. Cathala G.
TitleInvolvement of U1 small nuclear ribonucleoproteins (snRNP) in 5' splice site-U1 snRNP interaction.
SourceJ. Biol. Chem. 271:23985-23991(1996).
PubMed ID8798632

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