Human Gene UFM1 (ENST00000239878.9) from GENCODE V44
  Description: Homo sapiens ubiquitin fold modifier 1 (UFM1), transcript variant 7, non-coding RNA. (from RefSeq NR_104585)
RefSeq Summary (NM_016617): UFM1 is a ubiquitin-like protein that is conjugated to target proteins by E1-like activating enzyme UBA5 (UBE1DC1; MIM 610552) and E2-like conjugating enzyme UFC1 (MIM 610554) in a manner analogous to ubiquitylation (see UBE2M; MIM 603173) (Komatsu et al., 2004 [PubMed 15071506]).[supplied by OMIM, Dec 2008].
Gencode Transcript: ENST00000239878.9
Gencode Gene: ENSG00000120686.12
Transcript (Including UTRs)
   Position: hg38 chr13:38,349,851-38,363,619 Size: 13,769 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr13:38,349,920-38,360,778 Size: 10,859 Coding Exon Count: 6 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:38,349,851-38,363,619)mRNA (may differ from genome)Protein (85 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UFM1_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin-fold modifier 1; Flags: Precursor;
FUNCTION: Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1.
INTERACTION: Q96JB5:CDK5RAP3; NbExp=1; IntAct=EBI-1045061, EBI-718818;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Predominantly nuclear. Also expressed diffusely in the cytoplasm.
SIMILARITY: Belongs to the UFM1 family.

-  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           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.87 RPKM in Cells - Cultured fibroblasts
Total median expression: 1120.73 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 -18.8069-0.272 Picture PostScript Text
3' UTR -670.842841-0.236 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
IPR005375 - UFM1

Pfam Domains:
PF03671 - Ubiquitin fold modifier 1 protein

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WXS - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P61960
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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:0005515 protein binding

Biological Process:
GO:0033146 regulation of intracellular estrogen receptor signaling pathway
GO:0034976 response to endoplasmic reticulum stress
GO:0043066 negative regulation of apoptotic process
GO:0071569 protein ufmylation
GO:1990592 protein K69-linked ufmylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  AK307111 - Homo sapiens cDNA, FLJ97059.
AK095490 - Homo sapiens cDNA FLJ38171 fis, clone FCBBF1000025, highly similar to Homo sapiens BM-002 mRNA.
BC005193 - Homo sapiens ubiquitin-fold modifier 1, mRNA (cDNA clone MGC:12198 IMAGE:3829206), complete cds.
Z70222 - H.sapiens mRNA for ORF (clone ICRFp507G2490).
AF208844 - Homo sapiens BM-002 mRNA, complete cds.
AK309914 - Homo sapiens cDNA, FLJ99955.
JF432449 - Synthetic construct Homo sapiens clone IMAGE:100073660 ubiquitin-fold modifier 1 (UFM1) gene, encodes complete protein.
KJ898928 - Synthetic construct Homo sapiens clone ccsbBroadEn_08322 UFM1 gene, encodes complete protein.
AB154404 - Homo sapiens Ufm1 mRNA for Ubiquitin-fold modifier 1, complete cds.
CR457189 - Homo sapiens full open reading frame cDNA clone RZPDo834C128D for gene BM-002, hypothetical protein BM-002; complete cds, incl. stopcodon.
JD507044 - Sequence 488068 from Patent EP1572962.
AF369953 - Homo sapiens BIGMo-38 mRNA, partial sequence.
JD501952 - Sequence 482976 from Patent EP1572962.
JD112777 - Sequence 93801 from Patent EP1572962.
JD310024 - Sequence 291048 from Patent EP1572962.
JD147189 - Sequence 128213 from Patent EP1572962.
JD059776 - Sequence 40800 from Patent EP1572962.
JD170743 - Sequence 151767 from Patent EP1572962.
JD059075 - Sequence 40099 from Patent EP1572962.
JD224872 - Sequence 205896 from Patent EP1572962.
JD557177 - Sequence 538201 from Patent EP1572962.
JD038505 - Sequence 19529 from Patent EP1572962.
JD154594 - Sequence 135618 from Patent EP1572962.
JD243679 - Sequence 224703 from Patent EP1572962.
JD288152 - Sequence 269176 from Patent EP1572962.
JD213754 - Sequence 194778 from Patent EP1572962.
JD120054 - Sequence 101078 from Patent EP1572962.
JD268330 - Sequence 249354 from Patent EP1572962.
JD363601 - Sequence 344625 from Patent EP1572962.
JD566079 - Sequence 547103 from Patent EP1572962.
JD385530 - Sequence 366554 from Patent EP1572962.
JD053264 - Sequence 34288 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BM-002, C13orf20, ENST00000239878.1, ENST00000239878.2, ENST00000239878.3, ENST00000239878.4, ENST00000239878.5, ENST00000239878.6, ENST00000239878.7, ENST00000239878.8, NR_104585, P61960, Q14346, Q5VXS0, Q6IAG6, Q9CPX2, Q9NZF2, uc001uwu.1, uc001uwu.2, uc001uwu.3, uc001uwu.4, uc001uwu.5, uc001uwu.6, UFM1_HUMAN
UCSC ID: ENST00000239878.9
RefSeq Accession: NM_016617
Protein: P61960 (aka UFM1_HUMAN)
CCDS: CCDS9366.1

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