Human Gene RALGAPA1 (uc001wtj.3)
  Description: Homo sapiens Ral GTPase activating protein, alpha subunit 1 (catalytic) (RALGAPA1), transcript variant 2, mRNA.
RefSeq Summary (NM_194301): This gene encodes a major subunit of the RAL-GTPase activating protein. A similar protein in mouse binds E12, a transcriptional regulator of immunoglobulin genes. The mouse protein also functions in skeletal muscle by binding to the regulatory 14-3-3 proteins upon stimulation with insulin or muscle contraction. A pseudogene of this gene has been identified on chromosome 9. [provided by RefSeq, Oct 2016].
Transcript (Including UTRs)
   Position: hg19 chr14:36,007,558-36,278,432 Size: 270,875 Total Exon Count: 40 Strand: -
Coding Region
   Position: hg19 chr14:36,008,748-36,278,041 Size: 269,294 Coding Exon Count: 40 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:36,007,558-36,278,432)mRNA (may differ from genome)Protein (2083 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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): RALGAPA1
CDC HuGE Published Literature: RALGAPA1

-  MalaCards Disease Associations
  MalaCards Gene Search: RALGAPA1
Diseases sorted by gene-association score: holoprosencephaly 8 (10), ebola hemorrhagic fever (7)

-  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: 6.43 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 171.33 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 -223.70391-0.572 Picture PostScript Text
3' UTR -279.641190-0.235 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
  Pfam Domains:
PF02145 - Rap/ran-GAP

SCOP Domains:
111347 - Rap/Ran-GAP (Pfam 02145)

ModBase Predicted Comparative 3D Structure on Q6GYQ0-2
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  AY596970 - Homo sapiens tuberin-like protein 1 isoform 1 (GARNL1) mRNA, complete cds, alternatively spliced.
AY596971 - Homo sapiens tuberin-like protein 1 isoform 2 (GARNL1) mRNA, complete cds, alternatively spliced.
BC042013 - Homo sapiens GTPase activating Rap/RanGAP domain-like 1, mRNA (cDNA clone IMAGE:5311466), partial cds.
DQ786317 - Homo sapiens clone HLS_IMAGE_815163 mRNA sequence.
AL834362 - Homo sapiens mRNA; cDNA DKFZp667F074 (from clone DKFZp667F074).
AK126975 - Homo sapiens cDNA FLJ45028 fis, clone BRAWH3018063, highly similar to Rattus norvegicus tuberin-like protein 1 (Tulip1).
BC042045 - Homo sapiens GTPase activating Rap/RanGAP domain-like 1, mRNA (cDNA clone IMAGE:5527017), partial cds.
BC150596 - Homo sapiens GTPase activating Rap/RanGAP domain-like 1, mRNA (cDNA clone MGC:183506 IMAGE:9056966), complete cds.
AB511280 - Homo sapiens GARNL1 mRNA for RalGAP alpha1 catalytic subunit, complete cds.
BC168361 - Synthetic construct Homo sapiens clone IMAGE:100068257, MGC:195874 GTPase activating Rap/RanGAP domain-like 1 (GARNL1) mRNA, encodes complete protein.
AB020691 - Homo sapiens mRNA for KIAA0884 protein, partial cds.
AK022988 - Homo sapiens cDNA FLJ12926 fis, clone NT2RP2004732, weakly similar to NEUROFILAMENT TRIPLET M PROTEIN.
JD236984 - Sequence 218008 from Patent EP1572962.
JD245524 - Sequence 226548 from Patent EP1572962.
JD535953 - Sequence 516977 from Patent EP1572962.
JD563460 - Sequence 544484 from Patent EP1572962.
JD412232 - Sequence 393256 from Patent EP1572962.
JD564698 - Sequence 545722 from Patent EP1572962.
JD334453 - Sequence 315477 from Patent EP1572962.
JD159750 - Sequence 140774 from Patent EP1572962.
JD264813 - Sequence 245837 from Patent EP1572962.
JD429358 - Sequence 410382 from Patent EP1572962.
JD546470 - Sequence 527494 from Patent EP1572962.
JD553501 - Sequence 534525 from Patent EP1572962.
JD367952 - Sequence 348976 from Patent EP1572962.
JD263304 - Sequence 244328 from Patent EP1572962.
JD352810 - Sequence 333834 from Patent EP1572962.
JD444878 - Sequence 425902 from Patent EP1572962.
JD096485 - Sequence 77509 from Patent EP1572962.
JD067139 - Sequence 48163 from Patent EP1572962.
JD233507 - Sequence 214531 from Patent EP1572962.
JD306676 - Sequence 287700 from Patent EP1572962.
JD061867 - Sequence 42891 from Patent EP1572962.
JD490136 - Sequence 471160 from Patent EP1572962.
JD246030 - Sequence 227054 from Patent EP1572962.
JD081706 - Sequence 62730 from Patent EP1572962.
JD516077 - Sequence 497101 from Patent EP1572962.
JD422991 - Sequence 404015 from Patent EP1572962.
JD245004 - Sequence 226028 from Patent EP1572962.
JD350489 - Sequence 331513 from Patent EP1572962.
JD552861 - Sequence 533885 from Patent EP1572962.
JD364052 - Sequence 345076 from Patent EP1572962.
JD327322 - Sequence 308346 from Patent EP1572962.
BC016305 - Homo sapiens GTPase activating Rap/RanGAP domain-like 1, mRNA (cDNA clone IMAGE:4076117), partial cds.
JD206686 - Sequence 187710 from Patent EP1572962.
JD424546 - Sequence 405570 from Patent EP1572962.
JD351935 - Sequence 332959 from Patent EP1572962.
JD244494 - Sequence 225518 from Patent EP1572962.
JD102418 - Sequence 83442 from Patent EP1572962.
JD042492 - Sequence 23516 from Patent EP1572962.
JD495031 - Sequence 476055 from Patent EP1572962.
JD411204 - Sequence 392228 from Patent EP1572962.
JD301631 - Sequence 282655 from Patent EP1572962.
JD277471 - Sequence 258495 from Patent EP1572962.
JD401878 - Sequence 382902 from Patent EP1572962.
JD159882 - Sequence 140906 from Patent EP1572962.
JD037699 - Sequence 18723 from Patent EP1572962.
JD111537 - Sequence 92561 from Patent EP1572962.
JD264021 - Sequence 245045 from Patent EP1572962.
JD181869 - Sequence 162893 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: GARNL1, KIAA0884, NM_194301, NP_919277, Q6GYQ0-2, TULIP1
UCSC ID: uc001wtj.3
RefSeq Accession: NM_194301
Protein: Q6GYQ0-2, splice isoform of Q6GYQ0 CCDS: CCDS32065.1, CCDS61439.1, CCDS61440.1, CCDS32064.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_194301.2
exon count: 40CDS single in 3' UTR: no RNA size: 7851
ORF size: 6252CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 12695.00frame shift in genome: no % Coverage: 99.77
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.