Shroom3 Gene Detail

Summary

• Symbol
  Shroom3
• Name
  shroom family member 3
• Synonyms
  D5Ertd287e, Shrm, Shrm3

• Feature Type
  protein coding gene
• IDs
  MGI:1351655
  NCBI Gene: 27428
• Alliance
  gene page
• Transcription Start Sites
  29 TSS
• Candidate for QTL
  5 QTL

Location &
Maps

• Sequence Map
  Chr5:92831294-93113177 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 5, 47.29 cM, cytoband E3
• Mapping Data
  6 experiments

Strain
Comparison

• SNPs within 2kb
  8502 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1351655	protein coding gene	Chr5:92831294-93113618 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029756	protein coding gene	Chr5:93876608-94174341 (+)
A/J	MGP_AJ_G0029722	protein coding gene	Chr5:90139760-90427959 (+)
AKR/J	MGP_AKRJ_G0029668	protein coding gene	Chr5:93109927-93410490 (+)
BALB/cJ	MGP_BALBcJ_G0029732	protein coding gene	Chr5:91018321-91308351 (+)
C3H/HeJ	MGP_C3HHeJ_G0029455	protein coding gene	Chr5:93498818-93791379 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0030186	protein coding gene	Chr5:97594278-97912902 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027422	protein coding gene	Chr5:85778696-86065416 (+)
CAST/EiJ	MGP_CASTEiJ_G0028865	protein coding gene	Chr5:92876692-93178415 (+)
CBA/J	MGP_CBAJ_G0029425	protein coding gene	Chr5:101010645-101328904 (+)
DBA/2J	MGP_DBA2J_G0029569	protein coding gene	Chr5:90188954-90480701 (+)
FVB/NJ	MGP_FVBNJ_G0029528	protein coding gene	Chr5:89047320-89336492 (+)
LP/J	MGP_LPJ_G0029657	protein coding gene	Chr5:94237949-94544581 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029557	protein coding gene	Chr5:105890681-106210500 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0030220	protein coding gene	Chr5:92626935-92922959 (+)
PWK/PhJ	MGP_PWKPhJ_G0028584	protein coding gene	Chr5:89253064-89544935 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0028419	protein coding gene	Chr5:91963934-92262136 (+)
WSB/EiJ	MGP_WSBEiJ_G0028944	protein coding gene	Chr5:93085860-93388881 (+)

Homology

• Human Ortholog
  SHROOM3, shroom family member 3

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  SHROOM3, shroom family member 3
  
• Synonyms
  APXL3, MSTP013, SHRM, ShrmL
• Links
  HGNC:30422

  NCBI Gene ID: 57619

  neXtProt AC: NX_Q8TF72

  UniProt: Q8TF72

  
  
• Chr Location
  4q21.1; chr4:76435229-76783253 (+)  GRCh38

---

• MGI Vertebrate Homology
  Shroom3 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: SHROOM3
• Gene Tree
  Shroom3
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  31 phenotypes from 3 alleles in 4 genetic backgrounds
  4 phenotypes from multigenic genotypes
  36 phenotype references
  

• All Mutations and Alleles
  170
• Chemically induced (ENU)
  1
• Chemically induced (other)
  1
• Endonuclease-mediated
  4
• Gene trapped
  160
• Radiation induced
  1
• Spontaneous
  1
• Targeted
  2
• Genomic Mutations
  3 involving Shroom3
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  206 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype
• Recombinase Activity
  Comparison Matrix Gene Expression + Recombinase Activity

Homozygous mutation of this locus results in failed neural tube closure leading to exencephaly, acrania, facial clefting, and spina bifida. Homozygotes develop to term but die either at birth or shortly thereafter. Homozygotes for a gene trapped allele display congenital cardiac defects, as well as disrupted cardiomyocyte polarity, organization, proliferation and maturity.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  25
• GO References
  7

Expression

• Assay Results
  919
• Tissues
  76
• cDNA Data
  76
• Literature Summary
  20

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase shroom3
  ZFIN shroom3

Sequences &
Gene Models

• All Sequences
  78
• RefSeq
  10
• UniProt
  7
• CCDS
  CCDS39154.1, CCDS39155.1

• Ensembl
  ENSMUSG00000029381 (Evidence)
• NCBI Gene
  27428

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000029381	Ensembl Gene Model | MGI Sequence Detail	281884	C57BL/6J
transcript	ENSMUST00000113055	Ensembl | MGI Sequence Detail	6765	Not Applicable
polypeptide	ENSMUSP00000108678	Ensembl | MGI Sequence Detail	1980	Not Applicable

Protein
Information

• UniProt
  7 Sequences
• Protein Ontology
  PR:000014856 protein Shroom3
  (term hierarchy)
• InterPro Domains
  IPR014800 Apx/Shrm Domain 1
  IPR014799 Apx/Shrm Domain 2
  IPR001478 PDZ domain
  IPR036034 PDZ superfamily
  IPR027685 Shroom family
• GlyGen
  Q9QXN0 1 site, 1 O-linked glycan (1 site)

Molecular
Reagents

• All nucleic 80

  cDNA 77

  Primer pair 3

  
  

  Microarray probesets 8

Other
Accession IDs

MGI:1098648, MGI:2141015

References

• Summaries
  All 80

  Developmental Gene Expression 20

  Gene Ontology 7

  Phenotypes 36
• Earliest
  J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
• Latest
  J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Shroom3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr47322	Chr5:92830641-92830664 (+)	-641 bp
Tssr47323	Chr5:92831169-92831194 (+)	-112 bp
Tssr47324	Chr5:92831485-92831507 (+)	202 bp
Tssr47325	Chr5:92832696-92832700 (+)	1,404 bp
Tssr47326	Chr5:92957191-92957230 (+)	125,917 bp
Tssr47327	Chr5:92957231-92957295 (+)	125,969 bp
Tssr1548	Chr5:92965686-92965691 (+)	134,395 bp
Tssr47328	Chr5:92973670-92973710 (+)	142,396 bp
Tssr47329	Chr5:92973760-92973784 (+)	142,478 bp
Tssr47330	Chr5:92991530-92991534 (+)	160,238 bp
Tssr47331	Chr5:93004290-93004302 (+)	173,002 bp
Tssr47332	Chr5:93004313-93004324 (+)	173,025 bp
Tssr47333	Chr5:93004330-93004370 (+)	173,056 bp
Tssr47334	Chr5:93007302-93007331 (+)	176,023 bp
Tssr47335	Chr5:93024222-93024227 (+)	192,931 bp
Tssr47336	Chr5:93025546-93025550 (+)	194,254 bp
Tssr47337	Chr5:93045641-93045652 (+)	214,353 bp
Tssr47338	Chr5:93045815-93045833 (+)	214,530 bp
Tssr47339	Chr5:93045840-93045911 (+)	214,582 bp
Tssr47340	Chr5:93045912-93045934 (+)	214,629 bp
Tssr47341	Chr5:93046000-93046025 (+)	214,719 bp
Tssr47342	Chr5:93067481-93067525 (+)	236,209 bp
Tssr47343	Chr5:93073259-93073307 (+)	241,989 bp
Tssr47344	Chr5:93081176-93081196 (+)	249,892 bp
Tssr47345	Chr5:93087779-93087790 (+)	256,491 bp
Tssr47346	Chr5:93088388-93088413 (+)	257,107 bp
Tssr47347	Chr5:93102913-93102917 (+)	271,621 bp
Tssr47348	Chr5:93109927-93109952 (+)	278,646 bp
Tssr47349	Chr5:93110020-93110032 (+)	278,732 bp

Shroom3 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bw8	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Bw13	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Bwob	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Dbsty2	Chr5, 47.29 cM	Chr5:93445064-93445225	J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Igfbp3q1	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.

*cM position of peak correlated region/marker