Human Gene GCN1 (ENST00000300648.7_7) from GENCODE V47lift37
  Description: GCN1 activator of EIF2AK4 (from RefSeq NM_006836.2)
Gencode Transcript: ENST00000300648.7_7
Gencode Gene: ENSG00000089154.11_9
Transcript (Including UTRs)
   Position: hg19 chr12:120,565,006-120,632,518 Size: 67,513 Total Exon Count: 58 Strand: -
Coding Region
   Position: hg19 chr12:120,565,653-120,632,500 Size: 66,848 Coding Exon Count: 58 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:120,565,006-120,632,518)mRNA (may differ from genome)Protein (2671 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMalacards
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GCN1L_HUMAN
DESCRIPTION: RecName: Full=Translational activator GCN1; Short=HsGCN1; AltName: Full=GCN1-like protein 1;
FUNCTION: Acts as a translation activator that mediates translational control and perform an EF3-related function on the ribosome by regulating GCN2 protein kinase (EIF2AK1-4) activity (By similarity).
SUBUNIT: Interacts with IMPACT; prevents the interaction with GCN2 protein kinase (EIF2AK1-4) (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the GCN1 family.
SIMILARITY: Contains 24 HEAT repeats.
SEQUENCE CAUTION: Sequence=AAC51648.1; Type=Frameshift; Positions=2657; Sequence=AAC83183.1; Type=Erroneous gene model prediction; Sequence=BAA13209.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: GCN1
Diseases sorted by gene-association score: neuroblastoma (2)

+  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: 29.58 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 704.28 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 -1.6018-0.089 Picture PostScript Text
3' UTR -198.10647-0.306 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
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR000225 - Armadillo
IPR022716 - DUF3554
IPR026827 - ECM29/GCN1
IPR021133 - HEAT_type_2

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain

ModBase Predicted Comparative 3D Structure on Q92616
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0008135 translation factor activity, RNA binding
GO:0019887 protein kinase regulator activity
GO:0019901 protein kinase binding
GO:0043022 ribosome binding
GO:0045296 cadherin binding

Biological Process:
GO:0006412 translation
GO:0006417 regulation of translation
GO:0033554 cellular response to stress
GO:0033674 positive regulation of kinase activity
GO:0034198 cellular response to amino acid starvation
GO:0036003 positive regulation of transcription from RNA polymerase II promoter in response to stress
GO:0045859 regulation of protein kinase activity
GO:1990253 cellular response to leucine starvation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005844 polysome
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC153881 - Homo sapiens GCN1 general control of amino-acid synthesis 1-like 1 (yeast), mRNA (cDNA clone MGC:166916 IMAGE:8860118), complete cds.
D86973 - Homo sapiens mRNA for KIAA0219 gene.
U77700 - Homo sapiens HsGCN1 mRNA, partial cds.
BC113084 - Homo sapiens cDNA clone IMAGE:40071592.
BC113083 - Homo sapiens cDNA clone IMAGE:40071588.
AB587307 - Synthetic construct DNA, clone: pF1KA0219, Homo sapiens GCN1L1 gene for GCN1 general control of amino-acid synthesis 1-like 1, without stop codon, in Flexi system.
BC021129 - Homo sapiens, clone IMAGE:4622972, mRNA, partial cds.
BC046177 - Homo sapiens GCN1 general control of amino-acid synthesis 1-like 1 (yeast), mRNA (cDNA clone IMAGE:4441875), partial cds.
JD502346 - Sequence 483370 from Patent EP1572962.
BC064346 - Homo sapiens GCN1 general control of amino-acid synthesis 1-like 1 (yeast), mRNA (cDNA clone IMAGE:4442636), partial cds.
BC040172 - Homo sapiens, clone IMAGE:4470739, mRNA.
BC032335 - Homo sapiens, clone IMAGE:5181594, mRNA, partial cds.
U88836 - Human clone 738, translational activator GCN1 mRNA, partial cds.
JD564051 - Sequence 545075 from Patent EP1572962.
JD450983 - Sequence 432007 from Patent EP1572962.
JD300060 - Sequence 281084 from Patent EP1572962.
JD282450 - Sequence 263474 from Patent EP1572962.
JD146635 - Sequence 127659 from Patent EP1572962.
JD315232 - Sequence 296256 from Patent EP1572962.
JD263361 - Sequence 244385 from Patent EP1572962.
JD053366 - Sequence 34390 from Patent EP1572962.
JD083634 - Sequence 64658 from Patent EP1572962.
JD334037 - Sequence 315061 from Patent EP1572962.
JD254567 - Sequence 235591 from Patent EP1572962.
DL492361 - Novel nucleic acids.
DL490850 - Novel nucleic acids.
AK297271 - Homo sapiens cDNA FLJ54481 partial cds, highly similar to GCN1-like protein 1.
U88837 - Human clone 593, translational activator GCN1 mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: A8KAY1, ENST00000300648.1, ENST00000300648.2, ENST00000300648.3, ENST00000300648.4, ENST00000300648.5, ENST00000300648.6, GCN1 , GCN1L1 , GCN1_HUMAN, KIAA0219, NM_006836, O95001, O95651, Q6P2S3, Q86X65, Q8N5I5, Q8WU80, Q92616, Q99736, Q9UE60, uc317mqj.1, uc317mqj.2
UCSC ID: ENST00000300648.7_7
RefSeq Accession: NM_006836.2
Protein: Q92616 (aka GCN1L_HUMAN)

-  Gene Model Information
  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.