Shroom4 (shroom family member 4) - Rat Genome Database

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Gene: Shroom4 (shroom family member 4) Rattus norvegicus
Analyze
Symbol: Shroom4
Name: shroom family member 4
RGD ID: 1563434
Description: Predicted to enable actin filament binding activity and myosin II binding activity. Involved in regulation of postsynaptic membrane neurotransmitter receptor levels. Is active in several cellular components, including GABA-ergic synapse; glutamatergic synapse; and postsynapse. Orthologous to human SHROOM4 (shroom family member 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC317391; RGD1563434; similar to mKIAA1202 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X18,537,371 - 18,748,665 (-)NCBIGRCr8
mRatBN7.2X15,869,065 - 16,076,850 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX15,869,065 - 16,076,869 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX20,679,710 - 20,887,970 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X19,195,300 - 19,403,570 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X15,460,250 - 15,668,526 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X16,723,360 - 16,929,829 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX16,719,803 - 16,929,907 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X17,500,772 - 17,711,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X29,125,307 - 29,334,579 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX15,939,398 - 16,146,959 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. Epilepsy and intellectual disability linked protein Shrm4 interaction with GABABRs shapes inhibitory neurotransmission. Zapata J, etal., Nat Commun. 2017 Mar 6;8:14536. doi: 10.1038/ncomms14536.
Additional References at PubMed
PMID:16249884   PMID:16684770   PMID:17009331  


Genomics

Comparative Map Data
Shroom4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X18,537,371 - 18,748,665 (-)NCBIGRCr8
mRatBN7.2X15,869,065 - 16,076,850 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX15,869,065 - 16,076,869 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX20,679,710 - 20,887,970 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X19,195,300 - 19,403,570 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X15,460,250 - 15,668,526 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X16,723,360 - 16,929,829 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX16,719,803 - 16,929,907 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X17,500,772 - 17,711,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X29,125,307 - 29,334,579 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX15,939,398 - 16,146,959 (-)NCBICelera
Cytogenetic MapXq12NCBI
SHROOM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X50,575,534 - 50,814,194 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX50,586,796 - 50,814,302 (-)EnsemblGRCh38hg38GRCh38
GRCh37X50,329,796 - 50,557,194 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X50,351,387 - 50,573,784 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX54,378,231 - 54,600,597 (-)NCBICelera
Cytogenetic MapXp11.22NCBI
HuRefX47,778,364 - 48,000,648 (-)NCBIHuRef
CHM1_1X50,414,359 - 50,636,708 (-)NCBICHM1_1
T2T-CHM13v2.0X49,846,979 - 50,085,560 (-)NCBIT2T-CHM13v2.0
Shroom4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X6,312,012 - 6,549,508 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX6,311,908 - 6,549,502 (+)EnsemblGRCm39 Ensembl
GRCm38X6,399,949 - 6,637,454 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX6,399,854 - 6,637,448 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X5,977,263 - 6,210,835 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X5,575,508 - 5,812,930 (+)NCBIMGSCv36mm8
CeleraX4,778,748 - 5,011,260 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX2.85NCBI
Shroom4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555431,810,125 - 2,046,144 (-)NCBIChiLan1.0ChiLan1.0
SHROOM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X51,940,087 - 52,188,702 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X51,945,765 - 52,192,297 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X42,673,968 - 42,974,947 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X50,464,617 - 50,568,075 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX50,464,824 - 50,687,221 (-)Ensemblpanpan1.1panPan2
SHROOM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X43,366,921 - 43,639,525 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX43,369,472 - 43,639,302 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX17,743,343 - 18,016,771 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X43,486,469 - 43,759,942 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX43,487,462 - 43,760,464 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X43,490,284 - 43,763,685 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X43,478,265 - 43,751,712 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X43,573,217 - 43,846,683 (-)NCBIUU_Cfam_GSD_1.0
Shroom4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X35,828,330 - 36,037,677 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049367212,068,731 - 2,166,537 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHROOM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX44,332,620 - 44,543,337 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X44,301,956 - 44,543,969 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X49,298,058 - 49,474,957 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHROOM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X47,392,156 - 47,618,816 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX47,397,570 - 47,616,973 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666086984,033 - 1,212,187 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shroom4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248932,373,815 - 2,660,199 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248932,373,847 - 2,660,122 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shroom4
889 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:135
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000003971
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
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat

Markers in Region
AI407145  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X15,882,009 - 15,882,257 (+)MAPPERmRatBN7.2
Rnor_6.0X16,736,304 - 16,736,551NCBIRnor6.0
Rnor_5.0X17,517,258 - 17,517,505UniSTSRnor5.0
RGSC_v3.4X29,321,387 - 29,321,634UniSTSRGSC3.4
CeleraX15,952,343 - 15,952,590UniSTS
RH 3.4 MapX179.9UniSTS
Cytogenetic MapXq13UniSTS
BE107425  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X16,001,308 - 16,001,481 (+)MAPPERmRatBN7.2
Rnor_6.0X16,853,639 - 16,853,811NCBIRnor6.0
Rnor_5.0X17,635,783 - 17,635,955UniSTSRnor5.0
RGSC_v3.4X29,200,492 - 29,200,664UniSTSRGSC3.4
CeleraX16,071,740 - 16,071,912UniSTS
RH 3.4 MapX174.6UniSTS
Cytogenetic MapXq13UniSTS
AU049129  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X15,932,275 - 15,932,543 (+)MAPPERmRatBN7.2
Rnor_6.0X16,784,633 - 16,784,900NCBIRnor6.0
Rnor_5.0X17,567,455 - 17,567,722UniSTSRnor5.0
RGSC_v3.4X29,271,083 - 29,271,350UniSTSRGSC3.4
CeleraX16,002,773 - 16,003,040UniSTS
Cytogenetic MapXq13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000003971   ⟹   ENSRNOP00000003971
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX15,869,065 - 16,076,869 (-)Ensembl
Rnor_6.0 EnsemblX16,719,803 - 16,929,907 (-)Ensembl
RefSeq Acc Id: NM_001191730   ⟹   NP_001178659
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X18,540,913 - 18,748,515 (-)NCBI
mRatBN7.2X15,869,065 - 16,076,688 (-)NCBI
Rnor_6.0X16,723,360 - 16,929,829 (-)NCBI
Rnor_5.0X17,500,772 - 17,711,666 (-)NCBI
CeleraX15,939,398 - 16,146,959 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256763   ⟹   XP_006256825
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X18,537,371 - 18,588,941 (-)NCBI
mRatBN7.2X15,869,342 - 15,917,100 (-)NCBI
Rnor_6.0X16,723,637 - 16,769,603 (-)NCBI
Rnor_5.0X17,500,772 - 17,711,666 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602065   ⟹   XP_017457554
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X18,537,371 - 18,735,520 (-)NCBI
mRatBN7.2X15,869,342 - 16,075,779 (-)NCBI
Rnor_6.0X16,723,637 - 16,919,585 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099796   ⟹   XP_038955724
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X18,537,371 - 18,748,665 (-)NCBI
mRatBN7.2X15,869,342 - 16,076,850 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178659 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256825 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457554 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955724 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83868 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003971.6
RefSeq Acc Id: NP_001178659   ⟸   NM_001191730
- UniProtKB: F1LVL5 (UniProtKB/TrEMBL),   A6KPC0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256825   ⟸   XM_006256763
- Peptide Label: isoform X2
- UniProtKB: A6KPC0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457554   ⟸   XM_017602065
- Peptide Label: isoform X1
- UniProtKB: A6KPC0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003971   ⟸   ENSRNOT00000003971
RefSeq Acc Id: XP_038955724   ⟸   XM_039099796
- Peptide Label: isoform X1
- UniProtKB: A6KPC0 (UniProtKB/TrEMBL)
Protein Domains
ASD2   PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LVL5-F1-model_v2 AlphaFold F1LVL5 1-1487 view protein structure

Transcriptome

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

Promoters
RGD ID:13701754
Promoter ID:EPDNEW_R12278
Type:single initiation site
Name:Shroom4_1
Description:shroom family member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X16,929,931 - 16,929,991EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563434 AgrOrtholog
BioCyc Gene G2FUF-2872 BioCyc
Ensembl Genes ENSRNOG00000002959 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003971.8 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
  6.10.250.3120 UniProtKB/TrEMBL
InterPro ASD2 UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  Shroom_fam UniProtKB/TrEMBL
KEGG Report rno:317391 UniProtKB/TrEMBL
NCBI Gene 317391 ENTREZGENE
PANTHER PTHR15012 UniProtKB/TrEMBL
  PTHR15012:SF35 UniProtKB/TrEMBL
Pfam ASD2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PhenoGen Shroom4 PhenoGen
PROSITE ASD2 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002959 RatGTEx
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A6KPC0 ENTREZGENE, UniProtKB/TrEMBL
  F1LVL5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Shroom4  shroom family member 4  RGD1563434_predicted  similar to mKIAA1202 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563434_predicted  similar to mKIAA1202 protein (predicted)  LOC317391  similar to mKIAA1202 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317391  similar to mKIAA1202 protein      Symbol and Name status set to provisional 70820 PROVISIONAL