Lrch2 (leucine rich repeats and calponin homology domain containing 2) - Rat Genome Database

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Gene: Lrch2 (leucine rich repeats and calponin homology domain containing 2) Rattus norvegicus
Analyze
Symbol: Lrch2
Name: leucine rich repeats and calponin homology domain containing 2
RGD ID: 1590569
Description: Orthologous to human LRCH2 (leucine rich repeats and calponin homology domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: leucine-rich repeat and calponin homology domain-containing protein 2; leucine-rich repeats and calponin homology (CH) domain containing 2; leucine-rich repeats and calponin homology (CH) domain containing 2-like; LOC367754; LOC680591; similar to leucine-rich repeats and calponin homology (CH) domain containing 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX111,092,814 - 111,174,210 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X118,532,396 - 118,615,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX118,534,912 - 118,615,798 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X118,676,407 - 118,759,512 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X30,764,168 - 30,810,400 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX110,393,630 - 110,475,986 (-)NCBICelera
Cytogenetic MapXq34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21873635  


Genomics

Comparative Map Data
Lrch2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX111,092,814 - 111,174,210 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X118,532,396 - 118,615,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX118,534,912 - 118,615,798 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X118,676,407 - 118,759,512 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X30,764,168 - 30,810,400 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX110,393,630 - 110,475,986 (-)NCBICelera
Cytogenetic MapXq34NCBI
LRCH2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X115,110,616 - 115,234,096 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX115,110,616 - 115,234,096 (-)EnsemblGRCh38hg38GRCh38
GRCh37X114,345,179 - 114,468,659 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X114,251,435 - 114,374,891 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X114,168,161 - 114,291,615NCBI
CeleraX114,780,355 - 114,903,805 (-)NCBICelera
Cytogenetic MapXq23NCBI
HuRefX103,930,501 - 104,053,588 (-)NCBIHuRef
CHM1_1X114,256,054 - 114,379,667 (-)NCBICHM1_1
T2T-CHM13v2.0X113,519,325 - 113,642,681 (-)NCBIT2T-CHM13v2.0
Lrch2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X146,253,376 - 146,337,198 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX146,253,371 - 146,337,077 (-)EnsemblGRCm39 Ensembl
GRCm38X147,470,375 - 147,554,103 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX147,470,375 - 147,554,081 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X143,906,237 - 143,988,624 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X142,716,746 - 142,800,449 (-)NCBIMGSCv36mm8
CeleraX131,409,354 - 131,491,555 (-)NCBICelera
Cytogenetic MapXF2NCBI
cM MapX68.46NCBI
Lrch2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955490571,679 - 676,059 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955490569,526 - 678,626 (+)NCBIChiLan1.0ChiLan1.0
LRCH2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X114,557,752 - 114,681,184 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X104,201,087 - 104,324,505 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X114,705,457 - 114,828,080 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX114,717,260 - 114,828,080 (-)Ensemblpanpan1.1panPan2
LRCH2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X87,865,007 - 87,968,658 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX87,866,969 - 87,968,883 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX73,987,375 - 74,111,357 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X89,582,527 - 89,705,174 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX89,582,549 - 89,683,017 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X87,025,537 - 87,149,668 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X88,699,900 - 88,823,764 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X88,532,967 - 88,658,326 (-)NCBIUU_Cfam_GSD_1.0
Lrch2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X86,882,091 - 87,015,704 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936499673,274 - 775,868 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936499673,276 - 775,860 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LRCH2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX94,486,564 - 94,589,899 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X94,486,560 - 94,589,930 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X109,048,868 - 109,123,061 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LRCH2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X102,693,508 - 102,817,076 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX102,693,458 - 102,817,001 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606528,043,377 - 28,172,010 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lrch2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624940613,089 - 711,683 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624940612,992 - 712,284 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lrch2
294 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:98
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000041935, ENSRNOT00000044010, ENSRNOT00000045463
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 8 4 4 4 69 18 31
Low 3 29 20 10 6 10 6 6 5 8 8 7 6
Below cutoff 6 24 18 11 18 2 3 9 2 4 2

Sequence


RefSeq Acc Id: ENSRNOT00000045463   ⟹   ENSRNOP00000038957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX111,092,814 - 111,174,210 (-)Ensembl
Rnor_6.0 EnsemblX118,534,912 - 118,615,798 (-)Ensembl
RefSeq Acc Id: XM_001057911   ⟹   XP_001057911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
Rnor_6.0X118,532,396 - 118,615,845 (-)NCBI
Rnor_5.0X118,676,407 - 118,759,512 (-)NCBI
RGSC_v3.4X30,764,168 - 30,810,400 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257439   ⟹   XP_006257501
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
Rnor_6.0X118,532,396 - 118,615,845 (-)NCBI
Rnor_5.0X118,676,407 - 118,759,512 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100174   ⟹   XP_038956102
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
RefSeq Acc Id: XM_039100175   ⟹   XP_038956103
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
RefSeq Acc Id: XM_039100176   ⟹   XP_038956104
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
RefSeq Acc Id: XM_039100177   ⟹   XP_038956105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X111,091,728 - 111,174,225 (-)NCBI
RefSeq Acc Id: XP_001057911   ⟸   XM_001057911
- Peptide Label: isoform X3
- UniProtKB: D4A456 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257501   ⟸   XM_006257439
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000038957   ⟸   ENSRNOT00000045463
RefSeq Acc Id: XP_038956105   ⟸   XM_039100177
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038956104   ⟸   XM_039100176
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038956103   ⟸   XM_039100175
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956102   ⟸   XM_039100174
- Peptide Label: isoform X1
Protein Domains
Calponin-homology (CH)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A456-F1-model_v2 AlphaFold D4A456 1-772 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590569 AgrOrtholog
BioCyc Gene G2FUF-1441 BioCyc
Ensembl Genes ENSRNOG00000029582 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045463 ENTREZGENE
  ENSRNOT00000045463.5 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
KEGG Report rno:680591 UniProtKB/TrEMBL
NCBI Gene 680591 ENTREZGENE
PANTHER LEUCINE RICH REPEATS AND CALPONIN HOMOLOGY DOMAIN CONTAINING 2 UniProtKB/TrEMBL
  PTHR48051 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
  PF00307 UniProtKB/TrEMBL
PhenoGen Lrch2 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
  PS50021 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029582 RatGTEx
SMART LRR_BAC UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
  SM00033 UniProtKB/TrEMBL
Superfamily-SCOP Calponin-homology UniProtKB/TrEMBL
  L domain-like UniProtKB/TrEMBL
UniProt D4A456 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-15 Lrch2  leucine rich repeats and calponin homology domain containing 2  Lrch2  leucine-rich repeats and calponin homology (CH) domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Lrch2  leucine-rich repeats and calponin homology (CH) domain containing 2  LOC100364747  leucine-rich repeats and calponin homology (CH) domain containing 2-like  Data merged from RGD:2320416 1643240 APPROVED
2013-05-24 Lrch2  leucine-rich repeats and calponin homology (CH) domain containing 2  LOC100362509  leucine-rich repeats and calponin homology (CH) domain containing 2  Data merged from RGD:2324545 1643240 APPROVED
2010-05-06 LOC100362509  leucine-rich repeats and calponin homology (CH) domain containing 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-05 LOC100364747  leucine-rich repeats and calponin homology (CH) domain containing 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-05 Lrch2  leucine-rich repeats and calponin homology (CH) domain containing 2  LOC680591  similar to leucine-rich repeats and calponin homology (CH) domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC680591  similar to leucine-rich repeats and calponin homology (CH) domain containing 2  RGD1562632_predicted  similar to leucine-rich repeats and calponin homology (CH) domain containing 2 (predicted)  Data merged from RGD:1562632 1643240 APPROVED
2006-11-20 LOC680591  similar to leucine-rich repeats and calponin homology (CH) domain containing 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1562632_predicted  similar to leucine-rich repeats and calponin homology (CH) domain containing 2 (predicted)  LOC367754  similar to leucine-rich repeats and calponin homology (CH) domain containing 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367754  similar to leucine-rich repeats and calponin homology (CH) domain containing 2      Symbol and Name status set to provisional 70820 PROVISIONAL