Human Gene GRHL2 (uc010mbu.3) Description and Page Index
  Description: Homo sapiens grainyhead-like 2 (Drosophila) (GRHL2), mRNA.
RefSeq Summary (NM_024915): The protein encoded by this gene is a transcription factor that can act as a homodimer or as a heterodimer with either GRHL1 or GRHL3. Defects in this gene are a cause of non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28).[provided by RefSeq, Mar 2009]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because transcript sequence consistent with the reference genome assembly was not available for all regions of the RefSeq transcript. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK023844.1, BC129822.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1968832 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000646743.1/ ENSP00000495564.1 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:102,504,668-102,681,952 Size: 177,285 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr8:102,504,998-102,678,931 Size: 173,934 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:102,504,668-102,681,952)mRNA (may differ from genome)Protein (625 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: GRHL2_HUMAN
DESCRIPTION: RecName: Full=Grainyhead-like protein 2 homolog; AltName: Full=Brother of mammalian grainyhead; AltName: Full=Transcription factor CP2-like 3;
FUNCTION: May function as a transcription factor.
SUBUNIT: Homodimer, also forms heterodimers with GRHL1 or GRHL3.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Highly expressed in placenta, prostate, brain and kidney. Lower-level expression in a variety of epithelial tissues such as thymus, kidney, lung, salivary gland, mammary gland and digestive tract. Expressed in the cochlear.
DISEASE: Defects in GRHL2 are the cause of deafness autosomal dominant type 28 (DFNA28) [MIM:608641]. DFNA28 is a form of sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA28 is characterized by mild to moderate hearing loss across most frequencies that progressed to severe loss in the higher frequencies by the fifth decade. Age at onset varied, with the earliest case documented at 7 years of age.
SIMILARITY: Belongs to the grh/CP2 family. Grainyhead subfamily.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GRHL2
CDC HuGE Published Literature: GRHL2

-  MalaCards Disease Associations
  MalaCards Gene Search: GRHL2
Diseases sorted by gene-association score: ectodermal dysplasia/short stature syndrome* (1680), deafness, autosomal dominant 28* (937), dfna28 nonsyndromic hearing loss and deafness* (100), autosomal dominant non-syndromic sensorineural deafness type dfna* (60), poikiloderma with neutropenia (8), dubowitz syndrome (6), deafness, autosomal dominant 10 (6), dyskeratosis congenita (3)
* = Manually curated disease association

-  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: 16.88 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 120.41 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 -132.30330-0.401 Picture PostScript Text
3' UTR -1081.043021-0.358 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
IPR007604 - CP2

Pfam Domains:
PF04516 - CP2 transcription factor

ModBase Predicted Comparative 3D Structure on Q6ISB3
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001161 intronic transcription regulatory region sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0031490 chromatin DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001701 in utero embryonic development
GO:0001843 neural tube closure
GO:0003208 cardiac ventricle morphogenesis
GO:0003382 epithelial cell morphogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007155 cell adhesion
GO:0007420 brain development
GO:0008283 cell proliferation
GO:0008544 epidermis development
GO:0010468 regulation of gene expression
GO:0021915 neural tube development
GO:0030323 respiratory tube development
GO:0034329 cell junction assembly
GO:0035264 multicellular organism growth
GO:0042733 embryonic digit morphogenesis
GO:0043010 camera-type eye development
GO:0044030 regulation of DNA methylation
GO:0045617 negative regulation of keratinocyte differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048568 embryonic organ development
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0051973 positive regulation of telomerase activity
GO:0060324 face development
GO:0060463 lung lobe morphogenesis
GO:0060487 lung epithelial cell differentiation
GO:0060672 epithelial cell morphogenesis involved in placental branching
GO:0070830 bicellular tight junction assembly
GO:0090132 epithelium migration

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005911 cell-cell junction
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK292853 - Homo sapiens cDNA FLJ77442 complete cds, highly similar to Homo sapiens grainyhead-like 2 (Drosophila), mRNA.
BC069618 - Homo sapiens grainyhead-like 2 (Drosophila), mRNA (cDNA clone MGC:97148 IMAGE:7262389), complete cds.
BC069633 - Homo sapiens grainyhead-like 2 (Drosophila), mRNA (cDNA clone MGC:97159 IMAGE:7262401), complete cds.
BC069638 - Homo sapiens grainyhead-like 2 (Drosophila), mRNA (cDNA clone MGC:97170 IMAGE:7262413), complete cds.
BC129822 - Homo sapiens grainyhead-like 2 (Drosophila), mRNA (cDNA clone MGC:149294 IMAGE:40113571), complete cds.
BC129823 - Homo sapiens grainyhead-like 2 (Drosophila), mRNA (cDNA clone MGC:149295 IMAGE:40113576), complete cds.
AK023844 - Homo sapiens cDNA FLJ13782 fis, clone PLACE4000489, weakly similar to PROTEIN GRAINY-HEAD.
AB528018 - Synthetic construct DNA, clone: pF1KB7854, Homo sapiens GRHL2 gene for grainyhead-like protein 2, without stop codon, in Flexi system.
KJ894763 - Synthetic construct Homo sapiens clone ccsbBroadEn_04157 GRHL2 gene, encodes complete protein.
LF210250 - JP 2014500723-A/17753: Polycomb-Associated Non-Coding RNAs.
LF213362 - JP 2014500723-A/20865: Polycomb-Associated Non-Coding RNAs.
LF212600 - JP 2014500723-A/20103: Polycomb-Associated Non-Coding RNAs.
AK296817 - Homo sapiens cDNA FLJ53801 complete cds, highly similar to Grainyhead-like protein 2.
AK310221 - Homo sapiens cDNA, FLJ17263.
LF336146 - JP 2014500723-A/143649: Polycomb-Associated Non-Coding RNAs.
LF336147 - JP 2014500723-A/143650: Polycomb-Associated Non-Coding RNAs.
DQ600287 - Homo sapiens piRNA piR-38353, complete sequence.
MA445827 - JP 2018138019-A/17753: Polycomb-Associated Non-Coding RNAs.
MA448939 - JP 2018138019-A/20865: Polycomb-Associated Non-Coding RNAs.
MA448177 - JP 2018138019-A/20103: Polycomb-Associated Non-Coding RNAs.
MA571723 - JP 2018138019-A/143649: Polycomb-Associated Non-Coding RNAs.
MA571724 - JP 2018138019-A/143650: Polycomb-Associated Non-Coding RNAs.
AK002034 - Homo sapiens cDNA FLJ11172 fis, clone PLACE1007342.
JD475600 - Sequence 456624 from Patent EP1572962.
JD420843 - Sequence 401867 from Patent EP1572962.
JD442121 - Sequence 423145 from Patent EP1572962.
JD273024 - Sequence 254048 from Patent EP1572962.
JD335514 - Sequence 316538 from Patent EP1572962.
JD124707 - Sequence 105731 from Patent EP1572962.
JD117483 - Sequence 98507 from Patent EP1572962.
JD518881 - Sequence 499905 from Patent EP1572962.
JD101760 - Sequence 82784 from Patent EP1572962.
JD166496 - Sequence 147520 from Patent EP1572962.
JD502966 - Sequence 483990 from Patent EP1572962.
JD097956 - Sequence 78980 from Patent EP1572962.
JD240205 - Sequence 221229 from Patent EP1572962.
JD283011 - Sequence 264035 from Patent EP1572962.
JD188169 - Sequence 169193 from Patent EP1572962.
JD286878 - Sequence 267902 from Patent EP1572962.
JD136467 - Sequence 117491 from Patent EP1572962.
JD177726 - Sequence 158750 from Patent EP1572962.
JD290909 - Sequence 271933 from Patent EP1572962.
JD490311 - Sequence 471335 from Patent EP1572962.
JD255401 - Sequence 236425 from Patent EP1572962.
JD227807 - Sequence 208831 from Patent EP1572962.
JD245042 - Sequence 226066 from Patent EP1572962.
JD274170 - Sequence 255194 from Patent EP1572962.
JD322849 - Sequence 303873 from Patent EP1572962.
JD202808 - Sequence 183832 from Patent EP1572962.
JD250154 - Sequence 231178 from Patent EP1572962.
JD077748 - Sequence 58772 from Patent EP1572962.
JD283042 - Sequence 264066 from Patent EP1572962.
JD209953 - Sequence 190977 from Patent EP1572962.
JD456879 - Sequence 437903 from Patent EP1572962.
JD420932 - Sequence 401956 from Patent EP1572962.
JD541048 - Sequence 522072 from Patent EP1572962.
JD068264 - Sequence 49288 from Patent EP1572962.
JD235981 - Sequence 217005 from Patent EP1572962.
JD206824 - Sequence 187848 from Patent EP1572962.
JD150434 - Sequence 131458 from Patent EP1572962.
JD073139 - Sequence 54163 from Patent EP1572962.
JD153561 - Sequence 134585 from Patent EP1572962.
JD549981 - Sequence 531005 from Patent EP1572962.
JD095218 - Sequence 76242 from Patent EP1572962.
JD061406 - Sequence 42430 from Patent EP1572962.
JD049751 - Sequence 30775 from Patent EP1572962.
JD533225 - Sequence 514249 from Patent EP1572962.
JD304053 - Sequence 285077 from Patent EP1572962.
JD562310 - Sequence 543334 from Patent EP1572962.
JD379890 - Sequence 360914 from Patent EP1572962.
JD267242 - Sequence 248266 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A1L303, BOM, GRHL2_HUMAN, NM_024915, NP_079191, Q6ISB3, Q6NT03, Q9H8B8, TFCP2L3
UCSC ID: uc010mbu.3
RefSeq Accession: NM_024915
Protein: Q6ISB3 (aka GRHL2_HUMAN)
CCDS: CCDS34931.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GRHL2:
deafness-overview (Hereditary Hearing Loss and Deafness Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024915.3
exon count: 16CDS single in 3' UTR: no RNA size: 5231
ORF size: 1878CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3919.00frame shift in genome: no % Coverage: 99.96
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.