Human Gene CELSR1 (uc003bhw.1) Description and Page Index
  Description: Homo sapiens cadherin, EGF LAG seven-pass G-type receptor 1 (CELSR1), mRNA.
RefSeq Summary (NM_014246): The protein encoded by this gene is a member of the flamingo subfamily, part of the cadherin superfamily. The flamingo subfamily consists of nonclassic-type cadherins; a subpopulation that does not interact with catenins. The flamingo cadherins are located at the plasma membrane and have nine cadherin domains, seven epidermal growth factor-like repeats and two laminin A G-type repeats in their ectodomain. They also have seven transmembrane domains, a characteristic unique to this subfamily. It is postulated that these proteins are receptors involved in contact-mediated communication, with cadherin domains acting as homophilic binding regions and the EGF-like domains involved in cell adhesion and receptor-ligand interactions. This particular member is a developmentally regulated, neural-specific gene which plays an unspecified role in early embryogenesis. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on 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 :: AF231024.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr22:46,756,731-46,933,067 Size: 176,337 Total Exon Count: 35 Strand: -
Coding Region
   Position: hg19 chr22:46,759,075-46,933,067 Size: 173,993 Coding Exon Count: 35 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr22:46,756,731-46,933,067)mRNA (may differ from genome)Protein (3014 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cadherin EGF LAG seven-pass G-type receptor 1; AltName: Full=Cadherin family member 9; AltName: Full=Flamingo homolog 2; Short=hFmi2; Flags: Precursor;
FUNCTION: Receptor that may have an important role in cell/cell signaling during nervous system formation.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains (By similarity).
DISEASE: Defects in CELSR1 are a cause of neural tube defects (NTD) [MIM:182940]. NTD are congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components.
SIMILARITY: Belongs to the G-protein coupled receptor 2 family. LN-TM7 subfamily.
SIMILARITY: Contains 9 cadherin domains.
SIMILARITY: Contains 8 EGF-like domains.
SIMILARITY: Contains 1 GPS domain.
SIMILARITY: Contains 1 laminin EGF-like domain.
SIMILARITY: Contains 2 laminin G-like domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CELSR1
CDC HuGE Published Literature: CELSR1
Positive Disease Associations: Lipids , Stroke
Related Studies:
  1. Lipids
    , , . [PubMed 0]
  2. Stroke
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: CELSR1
Diseases sorted by gene-association score: neural tube defects* (133), myelomeningocele (12), anencephaly (9), craniorachischisis (9)
* = Manually curated disease association

-  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: 10.38 RPKM in Esophagus - Mucosa
Total median expression: 94.30 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
3' UTR -832.692344-0.355 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
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR022624 - DUF3497
IPR000742 - EG-like_dom
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR002049 - EGF_laminin
IPR017981 - GPCR_2-like
IPR001879 - GPCR_2_extracellular_dom
IPR000832 - GPCR_2_secretin-like
IPR000203 - GPS_dom
IPR001791 - Laminin_G

Pfam Domains:
PF00002 - 7 transmembrane receptor (Secretin family)
PF00008 - EGF-like domain
PF00028 - Cadherin domain
PF00053 - Laminin EGF domain
PF00054 - Laminin G domain
PF01825 - GPCR proteolysis site, GPS, motif
PF02210 - Laminin G domain
PF02793 - Hormone receptor domain
PF05462 - Slime mold cyclic AMP receptor
PF12661 - Human growth factor-like EGF
PF16489 - GPCR-Autoproteolysis INducing (GAIN) domain

SCOP Domains:
48371 - ARM repeat
49313 - Cadherin-like
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q9NYQ6
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     
  Protein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004888 transmembrane signaling receptor activity
GO:0004930 G-protein coupled receptor activity
GO:0005509 calcium ion binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0001736 establishment of planar polarity
GO:0001764 neuron migration
GO:0001843 neural tube closure
GO:0001942 hair follicle development
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007266 Rho protein signal transduction
GO:0007275 multicellular organism development
GO:0007417 central nervous system development
GO:0007626 locomotory behavior
GO:0009952 anterior/posterior pattern specification
GO:0032956 regulation of actin cytoskeleton organization
GO:0042060 wound healing
GO:0042249 establishment of planar polarity of embryonic epithelium
GO:0042472 inner ear morphogenesis
GO:0045176 apical protein localization
GO:0048105 establishment of body hair planar orientation
GO:0060071 Wnt signaling pathway, planar cell polarity pathway
GO:0060488 orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis
GO:0060489 planar dichotomous subdivision of terminal units involved in lung branching morphogenesis
GO:0060490 lateral sprouting involved in lung morphogenesis
GO:0090179 planar cell polarity pathway involved in neural tube closure
GO:0090251 protein localization involved in establishment of planar polarity

Cellular Component:
GO:0005654 nucleoplasm
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  AF231024 - Homo sapiens protocadherin Flamingo 2 (FMI2) mRNA, complete cds.
BC172920 - Synthetic construct Homo sapiens clone IMAGE:9094496 cadherin EGF LAG seven-pass G-type receptor 1 (CELSR1) gene, partial cds.
AK302517 - Homo sapiens cDNA FLJ51399 complete cds, highly similar to Cadherin EGF LAG seven-pass G-type receptor 1 precursor.
BC172919 - Synthetic construct Homo sapiens clone IMAGE:9094495 cadherin EGF LAG seven-pass G-type receptor 1 (CELSR1) gene, partial cds.
BC000059 - Homo sapiens cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Drosophila), mRNA (cDNA clone IMAGE:3506648), partial cds.
JD431457 - Sequence 412481 from Patent EP1572962.
JD261808 - Sequence 242832 from Patent EP1572962.
JD556563 - Sequence 537587 from Patent EP1572962.
JD120015 - Sequence 101039 from Patent EP1572962.
JD301113 - Sequence 282137 from Patent EP1572962.
JD378110 - Sequence 359134 from Patent EP1572962.
JD119455 - Sequence 100479 from Patent EP1572962.
BC013631 - Homo sapiens cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Drosophila), mRNA (cDNA clone IMAGE:3447418).
AL831846 - Homo sapiens mRNA; cDNA DKFZp434P0729 (from clone DKFZp434P0729).
JD060344 - Sequence 41368 from Patent EP1572962.
JD296518 - Sequence 277542 from Patent EP1572962.
JD206016 - Sequence 187040 from Patent EP1572962.
JD236809 - Sequence 217833 from Patent EP1572962.
JD417938 - Sequence 398962 from Patent EP1572962.
JD089284 - Sequence 70308 from Patent EP1572962.
JD314336 - Sequence 295360 from Patent EP1572962.
JD048823 - Sequence 29847 from Patent EP1572962.
JD311490 - Sequence 292514 from Patent EP1572962.
JD394559 - Sequence 375583 from Patent EP1572962.
JD373834 - Sequence 354858 from Patent EP1572962.
JD460167 - Sequence 441191 from Patent EP1572962.
JD115863 - Sequence 96887 from Patent EP1572962.
JD416068 - Sequence 397092 from Patent EP1572962.
JD100779 - Sequence 81803 from Patent EP1572962.
JD343660 - Sequence 324684 from Patent EP1572962.
JD343659 - Sequence 324683 from Patent EP1572962.
JD227132 - Sequence 208156 from Patent EP1572962.
JD423941 - Sequence 404965 from Patent EP1572962.
JD538518 - Sequence 519542 from Patent EP1572962.
JD426507 - Sequence 407531 from Patent EP1572962.
JD391111 - Sequence 372135 from Patent EP1572962.
JD434583 - Sequence 415607 from Patent EP1572962.
JD448710 - Sequence 429734 from Patent EP1572962.
JD391397 - Sequence 372421 from Patent EP1572962.
JD079958 - Sequence 60982 from Patent EP1572962.
JD175298 - Sequence 156322 from Patent EP1572962.
JD266744 - Sequence 247768 from Patent EP1572962.
JD311552 - Sequence 292576 from Patent EP1572962.
JD444209 - Sequence 425233 from Patent EP1572962.
JD489634 - Sequence 470658 from Patent EP1572962.
JD295143 - Sequence 276167 from Patent EP1572962.
JD078852 - Sequence 59876 from Patent EP1572962.
JD131635 - Sequence 112659 from Patent EP1572962.
JD538121 - Sequence 519145 from Patent EP1572962.
JD143014 - Sequence 124038 from Patent EP1572962.
JD310221 - Sequence 291245 from Patent EP1572962.
JD365548 - Sequence 346572 from Patent EP1572962.
JD151149 - Sequence 132173 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CDHF9, CELR1_HUMAN, FMI2, NM_014246, NP_055061, O95722, Q5TH47, Q9BWQ5, Q9NYQ6, Q9Y506, Q9Y526
UCSC ID: uc003bhw.1
RefSeq Accession: NM_014246
Protein: Q9NYQ6 (aka CELR1_HUMAN or CLR1_HUMAN)
CCDS: CCDS14076.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_014246.1
exon count: 35CDS single in 3' UTR: no RNA size: 11389
ORF size: 9045CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 14334.00frame shift in genome: no % Coverage: 100.00
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.