Human Gene MTHFSD (uc002fjo.3) Description and Page Index
  Description: Homo sapiens methenyltetrahydrofolate synthetase domain containing (MTHFSD), transcript variant 6, non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr16:86,563,782-86,588,841 Size: 25,060 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr16:86,565,617-86,575,772 Size: 10,156 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:86,563,782-86,588,841)mRNA (may differ from genome)Protein (220 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: MTHSD_HUMAN
DESCRIPTION: RecName: Full=Methenyltetrahydrofolate synthase domain-containing protein;
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=BAB14383.1; Type=Frameshift; Positions=356;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MTHFSD
CDC HuGE Published Literature: MTHFSD
Positive Disease Associations: smoking cessation
Related Studies:
  1. smoking cessation
    Uhl ,et al. Pharmacogenomics 2010, Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement , Pharmacogenomics 2010 11- 3 : 357-67. [PubMed 20235792]

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.32 RPKM in Testis
Total median expression: 167.99 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -192.93610-0.316 Picture PostScript Text
3' UTR -688.171835-0.375 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
IPR002698 - FTHF_cligase
IPR024185 - FTHF_cligase-like
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
100950 - NagB/RpiA/CoA transferase-like
54928 - RNA-binding domain, RBD

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

2E5J
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q2M296
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0008298 intracellular mRNA localization

Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK125015 - Homo sapiens cDNA FLJ43025 fis, clone BRTHA2018707.
AK096836 - Homo sapiens cDNA FLJ39517 fis, clone PUAEN2000394.
AK023060 - Homo sapiens cDNA FLJ12998 fis, clone NT2RP3000267.
JD143922 - Sequence 124946 from Patent EP1572962.
JD190124 - Sequence 171148 from Patent EP1572962.
AK023955 - Homo sapiens cDNA FLJ13893 fis, clone THYRO1001661.
JD565603 - Sequence 546627 from Patent EP1572962.
JD414289 - Sequence 395313 from Patent EP1572962.
JD408429 - Sequence 389453 from Patent EP1572962.
JD070091 - Sequence 51115 from Patent EP1572962.
JD304112 - Sequence 285136 from Patent EP1572962.
JD302501 - Sequence 283525 from Patent EP1572962.
JD442893 - Sequence 423917 from Patent EP1572962.
JD394298 - Sequence 375322 from Patent EP1572962.
JD062340 - Sequence 43364 from Patent EP1572962.
JD077279 - Sequence 58303 from Patent EP1572962.
JD342901 - Sequence 323925 from Patent EP1572962.
JD472766 - Sequence 453790 from Patent EP1572962.
JD214902 - Sequence 195926 from Patent EP1572962.
JD540938 - Sequence 521962 from Patent EP1572962.
DQ575061 - Homo sapiens piRNA piR-43173, complete sequence.
JD106375 - Sequence 87399 from Patent EP1572962.
JD317621 - Sequence 298645 from Patent EP1572962.
JD483662 - Sequence 464686 from Patent EP1572962.
JD248033 - Sequence 229057 from Patent EP1572962.
JD253660 - Sequence 234684 from Patent EP1572962.
JD126130 - Sequence 107154 from Patent EP1572962.
JD141639 - Sequence 122663 from Patent EP1572962.
JD057592 - Sequence 38616 from Patent EP1572962.
JD100685 - Sequence 81709 from Patent EP1572962.
BC112057 - Homo sapiens methenyltetrahydrofolate synthetase domain containing, mRNA (cDNA clone MGC:138262 IMAGE:8327525), complete cds.
BC112059 - Homo sapiens methenyltetrahydrofolate synthetase domain containing, mRNA (cDNA clone MGC:138264 IMAGE:8327527), complete cds.
BC143702 - Homo sapiens cDNA clone MGC:177233 IMAGE:9052216, complete cds.
BC143703 - Homo sapiens cDNA clone IMAGE:9052217, with apparent retained intron.
BC143704 - Homo sapiens cDNA clone IMAGE:9052218.
BC143705 - Homo sapiens cDNA clone IMAGE:9052219.
BC143707 - Homo sapiens methenyltetrahydrofolate synthetase domain containing, mRNA (cDNA clone MGC:177238 IMAGE:9052221), complete cds.
AK297726 - Homo sapiens cDNA FLJ61139 complete cds.
JD118683 - Sequence 99707 from Patent EP1572962.
JD159155 - Sequence 140179 from Patent EP1572962.
KJ899473 - Synthetic construct Homo sapiens clone ccsbBroadEn_08867 MTHFSD gene, encodes complete protein.
BC013911 - Homo sapiens methenyltetrahydrofolate synthetase domain containing, mRNA (cDNA clone IMAGE:4064921).

-  Other Names for This Gene
  Alternate Gene Symbols: A8MQ77, B7ZLC0, B7ZLC2, D3DUM9, E9PAM1, MTHSD_HUMAN, NR_027489, Q2M296, Q9H878, Q9H954
UCSC ID: uc002fjo.3
RefSeq Accession: NR_027489
Protein: Q2M296 (aka MTHSD_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_027489.1
exon count: 9CDS single in 3' UTR: no RNA size: 3108
ORF size: 663CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1093.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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