Human Gene ADAD1 (uc003ieq.3)
  Description: Homo sapiens adenosine deaminase domain containing 1 (testis-specific) (ADAD1), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:123,300,595-123,350,947 Size: 50,353 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr4:123,301,279-123,350,894 Size: 49,616 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:123,300,595-123,350,947)mRNA (may differ from genome)Protein (558 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ADAD1_HUMAN
DESCRIPTION: RecName: Full=Adenosine deaminase domain-containing protein 1; AltName: Full=Testis nuclear RNA-binding protein;
FUNCTION: Plays a role in spermatogenesis. Binds to RNA but not to DNA (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the ADAD family.
SIMILARITY: Contains 1 A to I editase domain.
SIMILARITY: Contains 1 DRBM (double-stranded RNA-binding) domain.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ADAD1
CDC HuGE Published Literature: ADAD1
Positive Disease Associations: Celiac disease , Colitis, Ulcerative , Diabetes Mellitus, Type 1
Related Studies:
  1. Celiac disease
    Hunt ,et al. 2008, Newly identified genetic risk variants for celiac disease related to the immune response, Nature genetics 2008 40- 4 : 395-402. [PubMed 18311140]
  2. Colitis, Ulcerative
    Carl A Anderson et al. Nature genetics 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47., Nature genetics. [PubMed 21297633]
  3. Diabetes Mellitus, Type 1
    Paul R Burton et al. Nature 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls., Nature. [PubMed 17554300]
           more ... click here to view the complete list

-  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: 66.97 RPKM in Testis
Total median expression: 66.97 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 -128.20272-0.471 Picture PostScript Text
3' UTR -6.4053-0.121 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
IPR002466 - A_deamin
IPR001159 - Ds-RNA-bd
IPR014720 - dsRNA-bd-like

Pfam Domains:
PF00035 - Double-stranded RNA binding motif
PF02137 - Adenosine-deaminase (editase) domain

SCOP Domains:
54768 - dsRNA-binding domain-like

ModBase Predicted Comparative 3D Structure on Q96M93
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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
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004000 adenosine deaminase activity

Biological Process:
GO:0006396 RNA processing
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK057303 - Homo sapiens cDNA FLJ32741 fis, clone TESTI2001345, highly similar to M.musculus Tenr mRNA for RNA binding protein.
HM005715 - Homo sapiens clone HTL-T-92mP testis tissue sperm-binding protein Li 92mP mRNA, complete cds.
BC040229 - Homo sapiens adenosine deaminase domain containing 1 (testis-specific), mRNA (cDNA clone MGC:35031 IMAGE:5164998), complete cds.
AK093297 - Homo sapiens cDNA FLJ35978 fis, clone TESTI2013497, highly similar to M.musculus Tenr mRNA for RNA binding protein.
AX748040 - Sequence 1565 from Patent EP1308459.
DQ893202 - Synthetic construct clone IMAGE:100005832; FLH195187.01X; RZPDo839E0784D testis nuclear RNA-binding protein (Tenr) gene, encodes complete protein.
DQ893203 - Synthetic construct clone IMAGE:100005833; FLH195188.01X; RZPDo839F0784D testis nuclear RNA-binding protein (Tenr) gene, encodes complete protein.
DQ896530 - Synthetic construct Homo sapiens clone IMAGE:100010990; FLH195183.01L; RZPDo839A0784D testis nuclear RNA-binding protein (Tenr) gene, encodes complete protein.
DQ896531 - Synthetic construct Homo sapiens clone IMAGE:100010991; FLH195185.01L; RZPDo839C0784D testis nuclear RNA-binding protein (Tenr) gene, encodes complete protein.
KJ904987 - Synthetic construct Homo sapiens clone ccsbBroadEn_14381 ADAD1-like gene, encodes complete protein.
CU691836 - Synthetic construct Homo sapiens gateway clone IMAGE:100019883 5' read ADAD1 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NKN4, ADAD1_HUMAN, B7WPB0, D3DNX2, NM_001159295, NP_001152767, Q8IWG6, Q8NA06, Q96M93, TENR
UCSC ID: uc003ieq.3
RefSeq Accession: NM_001159295
Protein: Q96M93 (aka ADAD1_HUMAN)
CCDS: CCDS54801.1, CCDS34058.1, CCDS54800.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001159295.1
exon count: 12CDS single in 3' UTR: no RNA size: 2012
ORF size: 1677CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3442.00frame shift in genome: no % Coverage: 99.50
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.