Human Gene ZMAT5 (ENST00000344318.4) from GENCODE V44
  Description: Homo sapiens zinc finger matrin-type 5 (ZMAT5), transcript variant 1, mRNA. (from RefSeq NM_019103)
Gencode Transcript: ENST00000344318.4
Gencode Gene: ENSG00000100319.13
Transcript (Including UTRs)
   Position: hg38 chr22:29,730,956-29,767,007 Size: 36,052 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr22:29,731,225-29,748,544 Size: 17,320 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:29,730,956-29,767,007)mRNA (may differ from genome)Protein (170 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMGIneXtProt
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZMAT5_HUMAN
DESCRIPTION: RecName: Full=Zinc finger matrin-type protein 5; AltName: Full=U11/U12 small nuclear ribonucleoprotein 20 kDa protein; Short=U11/U12 snRNP 20 kDa protein; Short=U11/U12-20K;
SUBUNIT: Component of the U11/U12 snRNPs that are part of the U12- type spliceosome. Not found in the major spliceosome.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 1 C3H1-type zinc finger.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.02 RPKM in Adrenal Gland
Total median expression: 621.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.30163-0.358 Picture PostScript Text
3' UTR -80.50269-0.299 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000571 - Znf_CCCH
IPR013085 - Znf_U1-C

Pfam Domains:
PF00642 - Zinc finger C-x8-C-x5-C-x3-H type (and similar)
PF06220 - U1 zinc finger

ModBase Predicted Comparative 3D Structure on Q9UDW3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AK292671 - Homo sapiens cDNA FLJ75820 complete cds, highly similar to Homo sapiens zinc finger, matrin type 5 (ZMAT5), transcript variant 2, mRNA.
BC009717 - Homo sapiens zinc finger, matrin type 5, mRNA (cDNA clone MGC:9510 IMAGE:3890730), complete cds.
AL160311 - Novel human gene mapping to chomosome 22.
AK123261 - Homo sapiens cDNA FLJ41267 fis, clone BRAMY2035923.
JD474879 - Sequence 455903 from Patent EP1572962.
JD483272 - Sequence 464296 from Patent EP1572962.
JD408335 - Sequence 389359 from Patent EP1572962.
JD227279 - Sequence 208303 from Patent EP1572962.
JD229548 - Sequence 210572 from Patent EP1572962.
JD364092 - Sequence 345116 from Patent EP1572962.
JD050760 - Sequence 31784 from Patent EP1572962.
JD189059 - Sequence 170083 from Patent EP1572962.
JD247519 - Sequence 228543 from Patent EP1572962.
JD387588 - Sequence 368612 from Patent EP1572962.
JD127690 - Sequence 108714 from Patent EP1572962.
JD396347 - Sequence 377371 from Patent EP1572962.
CR456353 - Homo sapiens Em:AC005529.5 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.Em:AC005529.5.V2).
KJ894290 - Synthetic construct Homo sapiens clone ccsbBroadEn_03684 ZMAT5 gene, encodes complete protein.
CU013063 - Homo sapiens ZMAT5, mRNA (cDNA clone IMAGE:100000322), complete cds, with stop codon, in Gateway system.
EU831804 - Synthetic construct Homo sapiens clone HAIB:100066833; DKFZo008E1221 zinc finger, matrin type 5 protein (ZMAT5) gene, encodes complete protein.
EU831881 - Synthetic construct Homo sapiens clone HAIB:100066910; DKFZo004E1222 zinc finger, matrin type 5 protein (ZMAT5) gene, encodes complete protein.
CU013351 - Homo sapiens ZMAT5, mRNA (cDNA clone IMAGE:100000226), complete cds, without stop codon, in Gateway system.
AB463380 - Synthetic construct DNA, clone: pF1KB9554, Homo sapiens ZMAT5 gene for zinc finger, matrin protein type 5, without stop codon, in Flexi system.
CR457393 - Homo sapiens full open reading frame cDNA clone RZPDo834F0710D for gene LOC55954, hypothetical protein LOC55954; complete cds, incl. stopcodon.
JD465397 - Sequence 446421 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UDW3 (Reactome details) participates in the following event(s):

R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9F6, ENST00000344318.1, ENST00000344318.2, ENST00000344318.3, NM_019103, Q9UDW3, uc003agn.1, uc003agn.2, uc003agn.3, uc003agn.4, uc003agn.5, ZMAT5_HUMAN
UCSC ID: ENST00000344318.4
RefSeq Accession: NM_001003692
Protein: Q9UDW3 (aka ZMAT5_HUMAN)
CCDS: CCDS13868.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.