Human Gene LRCH1 (ENST00000389797.8_7) from GENCODE V47lift37
  Description: leucine rich repeats and calponin homology domain containing 1, transcript variant 1 (from RefSeq NM_001164211.2)
Gencode Transcript: ENST00000389797.8_7
Gencode Gene: ENSG00000136141.15_16
Transcript (Including UTRs)
   Position: hg19 chr13:47,127,305-47,319,033 Size: 191,729 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr13:47,127,532-47,315,983 Size: 188,452 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:47,127,305-47,319,033)mRNA (may differ from genome)Protein (763 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LRCH1_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat and calponin homology domain-containing protein 1; AltName: Full=Calponin homology domain-containing protein 1; AltName: Full=Neuronal protein 81; Short=NP81;
SIMILARITY: Contains 1 CH (calponin-homology) domain.
SIMILARITY: Contains 9 LRR (leucine-rich) repeats.
SEQUENCE CAUTION: Sequence=BAA76860.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAH70793.1; Type=Erroneous gene model prediction; Sequence=CAH73643.1; Type=Erroneous gene model prediction; Sequence=CAI12229.1; Type=Erroneous gene model prediction;

-  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: LRCH1
Diseases sorted by gene-association score: osteoarthritis (4)

-  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: 22.18 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 291.27 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 -97.60227-0.430 Picture PostScript Text
3' UTR -842.803050-0.276 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
IPR001715 - CH-domain
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp

Pfam Domains:
PF00307 - Calponin homology (CH) domain
PF13855 - Leucine rich repeat

SCOP Domains:
47576 - Calponin-homology domain, CH-domain
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q9Y2L9
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 DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007165 signal transduction
GO:0034260 negative regulation of GTPase activity
GO:1990869 cellular response to chemokine
GO:2000405 negative regulation of T cell migration

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  LF210161 - JP 2014500723-A/17664: Polycomb-Associated Non-Coding RNAs.
AY050632 - Homo sapiens neuronal protein isoform B mRNA, complete cds.
AY050631 - Homo sapiens neuronal protein isoform a mRNA, complete cds.
AK309937 - Homo sapiens cDNA, FLJ99978.
AK292898 - Homo sapiens cDNA FLJ76690 complete cds, highly similar to Homo sapiens neuronal protein isoform a mRNA.
AB023233 - Homo sapiens KIAA1016 mRNA for KIAA1016 protein.
BC112937 - Homo sapiens leucine-rich repeats and calponin homology (CH) domain containing 1, mRNA (cDNA clone MGC:131868 IMAGE:5204613), complete cds.
BC117472 - Homo sapiens leucine-rich repeats and calponin homology (CH) domain containing 1, mRNA (cDNA clone MGC:151081 IMAGE:40126023), complete cds.
BC143883 - Homo sapiens leucine-rich repeats and calponin homology (CH) domain containing 1, mRNA (cDNA clone MGC:177416 IMAGE:9052399), complete cds.
AB385418 - Synthetic construct DNA, clone: pF1KA1016, Homo sapiens LRCH1 gene for leucine-rich repeat and calponin homology domain-containing protein 1, complete cds, without stop codon, in Flexi system.
HQ258591 - Synthetic construct Homo sapiens clone IMAGE:100073126 leucine-rich repeats and calponin homology (CH) domain containing 1 (LRCH1) gene, encodes complete protein.
KJ898447 - Synthetic construct Homo sapiens clone ccsbBroadEn_07841 LRCH1 gene, encodes complete protein.
MA445738 - JP 2018138019-A/17664: Polycomb-Associated Non-Coding RNAs.
BC026097 - Homo sapiens leucine-rich repeats and calponin homology (CH) domain containing 1, mRNA (cDNA clone IMAGE:4669781), partial cds.
AK123654 - Homo sapiens cDNA FLJ41660 fis, clone FEBRA2026879.
JD127845 - Sequence 108869 from Patent EP1572962.
JD057704 - Sequence 38728 from Patent EP1572962.
JD122881 - Sequence 103905 from Patent EP1572962.
JD055569 - Sequence 36593 from Patent EP1572962.
JD163074 - Sequence 144098 from Patent EP1572962.
JD111191 - Sequence 92215 from Patent EP1572962.
JD111496 - Sequence 92520 from Patent EP1572962.
JD123225 - Sequence 104249 from Patent EP1572962.
JD444984 - Sequence 426008 from Patent EP1572962.
JD429892 - Sequence 410916 from Patent EP1572962.
JD114481 - Sequence 95505 from Patent EP1572962.
JD304800 - Sequence 285824 from Patent EP1572962.
JD084652 - Sequence 65676 from Patent EP1572962.
JD372053 - Sequence 353077 from Patent EP1572962.
JD467092 - Sequence 448116 from Patent EP1572962.
JD161343 - Sequence 142367 from Patent EP1572962.
JD547330 - Sequence 528354 from Patent EP1572962.
JD520353 - Sequence 501377 from Patent EP1572962.
JD193962 - Sequence 174986 from Patent EP1572962.
JD307804 - Sequence 288828 from Patent EP1572962.
LF335216 - JP 2014500723-A/142719: Polycomb-Associated Non-Coding RNAs.
JD293883 - Sequence 274907 from Patent EP1572962.
JD268696 - Sequence 249720 from Patent EP1572962.
JD090250 - Sequence 71274 from Patent EP1572962.
JD288224 - Sequence 269248 from Patent EP1572962.
JD553029 - Sequence 534053 from Patent EP1572962.
JD109710 - Sequence 90734 from Patent EP1572962.
JD148066 - Sequence 129090 from Patent EP1572962.
JD397962 - Sequence 378986 from Patent EP1572962.
JD257898 - Sequence 238922 from Patent EP1572962.
JD496285 - Sequence 477309 from Patent EP1572962.
MA570793 - JP 2018138019-A/142719: Polycomb-Associated Non-Coding RNAs.
LF335202 - JP 2014500723-A/142705: Polycomb-Associated Non-Coding RNAs.
JD046557 - Sequence 27581 from Patent EP1572962.
JD182748 - Sequence 163772 from Patent EP1572962.
JD052586 - Sequence 33610 from Patent EP1572962.
JD092478 - Sequence 73502 from Patent EP1572962.
MA570779 - JP 2018138019-A/142705: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZLL5, CHDC1, ENST00000389797.1, ENST00000389797.2, ENST00000389797.3, ENST00000389797.4, ENST00000389797.5, ENST00000389797.6, ENST00000389797.7, F8W6F0, KIAA1016, LRCH1_HUMAN, NM_001164211, Q17R43, Q2KHR1, Q5TBU9, Q7Z5F6, Q7Z5F7, Q9Y2L9, uc318tib.1, uc318tib.2
UCSC ID: ENST00000389797.8_7
RefSeq Accession: NM_001164211.2
Protein: Q9Y2L9 (aka LRCH1_HUMAN or LRC1_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.