Human Gene SPTY2D1 (uc001moy.3) Description and Page Index
  Description: Homo sapiens SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) (SPTY2D1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:18,627,948-18,656,020 Size: 28,073 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr11:18,631,408-18,655,804 Size: 24,397 Coding Exon Count: 6 

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 (chr11:18,627,948-18,656,020)mRNA (may differ from genome)Protein (685 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Protein SPT2 homolog; AltName: Full=Protein KU002155; AltName: Full=SPT2 domain-containing protein 1;
SIMILARITY: Belongs to the SPT2 family.
SEQUENCE CAUTION: Sequence=AAP13351.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SPTY2D1
CDC HuGE Published Literature: SPTY2D1
Positive Disease Associations: Cholesterol , Coronary Artery Disease , Oocytes , Stroke
Related Studies:
  1. Cholesterol
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]
  2. Coronary Artery Disease
    , , . [PubMed 0]
  3. Oocytes
    Sonya M Schuh-Huerta et al. Human reproduction (Oxford, England) 2012, Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women., Human reproduction (Oxford, England). [PubMed 22116950]
    This work is the largest study on ovarian reserve in women of reproductive age and is the only genome-wide study on ovarian reserve markers. The genes containing or near the identified variants have no known roles in ovarian biology and represent interesting candidate genes for future investigations. The discovery of genetic markers may lead to better long-range predictions of declining ovarian function, with implications for reproductive and somatic health.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 10.80 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 184.66 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 -110.20216-0.510 Picture PostScript Text
3' UTR -945.833460-0.273 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
IPR013256 - Chromatin_SPT2

Pfam Domains:
PF08243 - SPT2 chromatin protein

ModBase Predicted Comparative 3D Structure on Q68D10
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 orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  Protein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001042 RNA polymerase I core binding
GO:0003677 DNA binding
GO:0042393 histone binding

Biological Process:
GO:0006334 nucleosome assembly
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0010847 regulation of chromatin assembly
GO:0043486 histone exchange

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005730 nucleolus

-  Descriptions from all associated GenBank mRNAs
  LF207688 - JP 2014500723-A/15191: Polycomb-Associated Non-Coding RNAs.
AL834393 - Homo sapiens mRNA; cDNA DKFZp761I1323 (from clone DKFZp761I1323).
CR749626 - Homo sapiens mRNA; cDNA DKFZp686F1942 (from clone DKFZp686F1942).
BX647798 - Homo sapiens mRNA; cDNA DKFZp686I068 (from clone DKFZp686I068).
AF086471 - Homo sapiens full length insert cDNA clone ZD88A01.
BX538046 - Homo sapiens mRNA; cDNA DKFZp686C04150 (from clone DKFZp686C04150).
AK096694 - Homo sapiens cDNA FLJ39375 fis, clone PEBLM2008826.
BC056261 - Homo sapiens SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae), mRNA (cDNA clone MGC:62001 IMAGE:6616686), complete cds.
KJ903825 - Synthetic construct Homo sapiens clone ccsbBroadEn_13219 SPTY2D1 gene, encodes complete protein.
BX641102 - Homo sapiens mRNA; cDNA DKFZp686H12245 (from clone DKFZp686H12245).
BX648478 - Homo sapiens mRNA; cDNA DKFZp686B1355 (from clone DKFZp686B1355).
JD112991 - Sequence 94015 from Patent EP1572962.
BX648114 - Homo sapiens mRNA; cDNA DKFZp686F1032 (from clone DKFZp686F1032).
JD294834 - Sequence 275858 from Patent EP1572962.
JD067636 - Sequence 48660 from Patent EP1572962.
JD507963 - Sequence 488987 from Patent EP1572962.
JD349019 - Sequence 330043 from Patent EP1572962.
JD182088 - Sequence 163112 from Patent EP1572962.
JD331580 - Sequence 312604 from Patent EP1572962.
JD044104 - Sequence 25128 from Patent EP1572962.
JD096299 - Sequence 77323 from Patent EP1572962.
JD370987 - Sequence 352011 from Patent EP1572962.
JD401697 - Sequence 382721 from Patent EP1572962.
JD322991 - Sequence 304015 from Patent EP1572962.
JD307114 - Sequence 288138 from Patent EP1572962.
JD434950 - Sequence 415974 from Patent EP1572962.
JD061894 - Sequence 42918 from Patent EP1572962.
JD472394 - Sequence 453418 from Patent EP1572962.
JD056409 - Sequence 37433 from Patent EP1572962.
JD239952 - Sequence 220976 from Patent EP1572962.
JD238316 - Sequence 219340 from Patent EP1572962.
JD135729 - Sequence 116753 from Patent EP1572962.
JD097663 - Sequence 78687 from Patent EP1572962.
JD050336 - Sequence 31360 from Patent EP1572962.
JD188642 - Sequence 169666 from Patent EP1572962.
JD208827 - Sequence 189851 from Patent EP1572962.
JD159031 - Sequence 140055 from Patent EP1572962.
JD105703 - Sequence 86727 from Patent EP1572962.
JD430834 - Sequence 411858 from Patent EP1572962.
JD430835 - Sequence 411859 from Patent EP1572962.
JD430833 - Sequence 411857 from Patent EP1572962.
JD430832 - Sequence 411856 from Patent EP1572962.
JD138927 - Sequence 119951 from Patent EP1572962.
JD348605 - Sequence 329629 from Patent EP1572962.
JD324660 - Sequence 305684 from Patent EP1572962.
JD258000 - Sequence 239024 from Patent EP1572962.
JD184109 - Sequence 165133 from Patent EP1572962.
JD088870 - Sequence 69894 from Patent EP1572962.
JD360577 - Sequence 341601 from Patent EP1572962.
JD477783 - Sequence 458807 from Patent EP1572962.
JD082202 - Sequence 63226 from Patent EP1572962.
JD467785 - Sequence 448809 from Patent EP1572962.
JD434132 - Sequence 415156 from Patent EP1572962.
JD328169 - Sequence 309193 from Patent EP1572962.
JD486482 - Sequence 467506 from Patent EP1572962.
JD314087 - Sequence 295111 from Patent EP1572962.
JD137243 - Sequence 118267 from Patent EP1572962.
JD442279 - Sequence 423303 from Patent EP1572962.
JD167338 - Sequence 148362 from Patent EP1572962.
JD064789 - Sequence 45813 from Patent EP1572962.
JD533368 - Sequence 514392 from Patent EP1572962.
JD552583 - Sequence 533607 from Patent EP1572962.
JD360468 - Sequence 341492 from Patent EP1572962.
JD550542 - Sequence 531566 from Patent EP1572962.
LF368006 - JP 2014500723-A/175509: Polycomb-Associated Non-Coding RNAs.
AF452716 - Homo sapiens clone KU002155 unknown mRNA.
BC036844 - Homo sapiens SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae), mRNA (cDNA clone IMAGE:5229445), partial cds.
LF368007 - JP 2014500723-A/175510: Polycomb-Associated Non-Coding RNAs.
LF368008 - JP 2014500723-A/175511: Polycomb-Associated Non-Coding RNAs.
JD353868 - Sequence 334892 from Patent EP1572962.
JD507466 - Sequence 488490 from Patent EP1572962.
LF368009 - JP 2014500723-A/175512: Polycomb-Associated Non-Coding RNAs.
AK304078 - Homo sapiens cDNA FLJ52075 complete cds, moderately similar to Mus musculus SPT2, Suppressor of Ty, domain containing 1, mRNA.
AK096760 - Homo sapiens cDNA FLJ39441 fis, clone PROST2005793.
LF368010 - JP 2014500723-A/175513: Polycomb-Associated Non-Coding RNAs.
LF368011 - JP 2014500723-A/175514: Polycomb-Associated Non-Coding RNAs.
LF368012 - JP 2014500723-A/175515: Polycomb-Associated Non-Coding RNAs.
LF368013 - JP 2014500723-A/175516: Polycomb-Associated Non-Coding RNAs.
LF368014 - JP 2014500723-A/175517: Polycomb-Associated Non-Coding RNAs.
LF368015 - JP 2014500723-A/175518: Polycomb-Associated Non-Coding RNAs.
LF207689 - JP 2014500723-A/15192: Polycomb-Associated Non-Coding RNAs.
JD520248 - Sequence 501272 from Patent EP1572962.
JD555225 - Sequence 536249 from Patent EP1572962.
JD487587 - Sequence 468611 from Patent EP1572962.
JD461633 - Sequence 442657 from Patent EP1572962.
MA603583 - JP 2018138019-A/175509: Polycomb-Associated Non-Coding RNAs.
MA603584 - JP 2018138019-A/175510: Polycomb-Associated Non-Coding RNAs.
MA603585 - JP 2018138019-A/175511: Polycomb-Associated Non-Coding RNAs.
MA603586 - JP 2018138019-A/175512: Polycomb-Associated Non-Coding RNAs.
MA603587 - JP 2018138019-A/175513: Polycomb-Associated Non-Coding RNAs.
MA603588 - JP 2018138019-A/175514: Polycomb-Associated Non-Coding RNAs.
MA603589 - JP 2018138019-A/175515: Polycomb-Associated Non-Coding RNAs.
MA603590 - JP 2018138019-A/175516: Polycomb-Associated Non-Coding RNAs.
MA603591 - JP 2018138019-A/175517: Polycomb-Associated Non-Coding RNAs.
MA603592 - JP 2018138019-A/175518: Polycomb-Associated Non-Coding RNAs.
MA443265 - JP 2018138019-A/15191: Polycomb-Associated Non-Coding RNAs.
MA443266 - JP 2018138019-A/15192: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_194285, NP_919261, Q68D10, Q6AWA5, Q6MZI5, Q7Z390, Q7Z470, Q86VG8, Q8N3E7, Q8N417, Q8N8I3, SPT2_HUMAN
UCSC ID: uc001moy.3
RefSeq Accession: NM_194285
Protein: Q68D10 (aka SPT2_HUMAN)
CCDS: CCDS31441.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_194285.2
exon count: 6CDS single in 3' UTR: no RNA size: 5752
ORF size: 2058CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4310.00frame shift in genome: no % Coverage: 99.69
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.