Human Gene ACTRT1 (uc004eum.3)
  Description: Homo sapiens actin-related protein T1 (ACTRT1), mRNA.
RefSeq Summary (NM_138289): This gene encodes a protein related to the cytoskeletal protein beta-actin. This protein is a major component of the calyx in the perinuclear theca of mammalian sperm heads, and it therefore likely functions in spermatid formation. This gene is intronless and is similar to a related gene located on chromosome 1. A related pseudogene has also been identified approximately 75 kb downstream of this gene on chromosome X. [provided by RefSeq, May 2010].
Transcript (Including UTRs)
   Position: hg19 chrX:127,184,941-127,186,382 Size: 1,442 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chrX:127,185,055-127,186,185 Size: 1,131 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:127,184,941-127,186,382)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ACTT1_HUMAN
DESCRIPTION: RecName: Full=Actin-related protein T1; Short=ARP-T1;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton (By similarity).
SIMILARITY: Belongs to the actin 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


+  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: 4.18 RPKM in Testis
Total median expression: 4.18 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 -49.33197-0.250 Picture PostScript Text
3' UTR -28.50114-0.250 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
IPR004000 - Actin-like

Pfam Domains:
PF00022 - Actin

SCOP Domains:
53067 - Actin-like ATPase domain

ModBase Predicted Comparative 3D Structure on Q8TDG2
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 Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  BC014597 - Homo sapiens actin-related protein T1, mRNA (cDNA clone MGC:26590 IMAGE:4825563), complete cds.
JD298815 - Sequence 279839 from Patent EP1572962.
JD176182 - Sequence 157206 from Patent EP1572962.
JD328840 - Sequence 309864 from Patent EP1572962.
AY251532 - Homo sapiens HSD27 mRNA, complete cds.
AF440739 - Homo sapiens actin-related protein T1 (ACTRT1) mRNA, complete cds.
KJ895538 - Synthetic construct Homo sapiens clone ccsbBroadEn_04932 ACTRT1 gene, encodes complete protein.
EU832175 - Synthetic construct Homo sapiens clone HAIB:100067204; DKFZo008H0625 actin-related protein T1 protein (ACTRT1) gene, encodes complete protein.
EU832268 - Synthetic construct Homo sapiens clone HAIB:100067297; DKFZo004H0626 actin-related protein T1 protein (ACTRT1) gene, encodes complete protein.
JD166619 - Sequence 147643 from Patent EP1572962.
JD257984 - Sequence 239008 from Patent EP1572962.
JD303121 - Sequence 284145 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ACTT1_HUMAN, ARPT1, HSD27, NM_138289, NP_612146, Q6X7C1, Q8TDG2, Q96L10
UCSC ID: uc004eum.3
RefSeq Accession: NM_138289
Protein: Q8TDG2 (aka ACTT1_HUMAN)
CCDS: CCDS14611.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138289.3
exon count: 1CDS single in 3' UTR: no RNA size: 1452
ORF size: 1131CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2233.00frame shift in genome: no % Coverage: 99.31
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.