Samd4b (sterile alpha motif domain containing 4B) - Rat Genome Database

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Gene: Samd4b (sterile alpha motif domain containing 4B) Mus musculus
Analyze
Symbol: Samd4b
Name: sterile alpha motif domain containing 4B
RGD ID: 1313720
MGI Page MGI
Description: Enables mRNA binding activity. Acts upstream of or within cerebellar neuron development. Predicted to be located in cytosol. Predicted to be active in P-body. Is expressed in cerebral cortex; cerebral cortex subventricular zone; cerebral cortex ventricular layer; cortical plate; and telencephalon. Orthologous to human SAMD4B (sterile alpha motif domain containing 4B); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; clobetasol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BC042901; MGC30302; mSmaug2; protein Smaug homolog 2; smaug 2; sterile alpha motif domain-containing protein 4B
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,098,947 - 28,135,616 (-)NCBIGRCm39mm39
GRCm39 Ensembl728,098,947 - 28,297,569 (-)Ensembl
GRCm38728,399,522 - 28,436,191 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,399,522 - 28,598,144 (-)EnsemblGRCm38mm10GRCm38
MGSCv37729,184,541 - 29,221,210 (-)NCBIGRCm37mm9NCBIm37
MGSCv36728,109,032 - 28,144,951 (-)NCBImm8
Celera722,961,111 - 22,997,787 (-)NCBICelera
Cytogenetic Map7A3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)
cytosol  (ISO)
nucleus  (IEA)
P-body  (IBA)

Molecular Function

References

Additional References at PubMed
PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15489334   PMID:15782199   PMID:16141072  
PMID:16141073   PMID:17967808   PMID:18799693   PMID:21267068   PMID:21873635   PMID:26609159   PMID:31138677  


Genomics

Comparative Map Data
Samd4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,098,947 - 28,135,616 (-)NCBIGRCm39mm39
GRCm39 Ensembl728,098,947 - 28,297,569 (-)Ensembl
GRCm38728,399,522 - 28,436,191 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,399,522 - 28,598,144 (-)EnsemblGRCm38mm10GRCm38
MGSCv37729,184,541 - 29,221,210 (-)NCBIGRCm37mm9NCBIm37
MGSCv36728,109,032 - 28,144,951 (-)NCBImm8
Celera722,961,111 - 22,997,787 (-)NCBICelera
Cytogenetic Map7A3NCBI
SAMD4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1939,342,396 - 39,385,710 (+)EnsemblGRCh38hg38GRCh38
GRCh381939,342,421 - 39,390,748 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371939,833,061 - 39,875,528 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361944,524,948 - 44,567,382 (+)NCBINCBI36hg18NCBI36
Celera1936,634,788 - 36,677,224 (+)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1936,279,807 - 36,322,244 (+)NCBIHuRef
CHM1_11939,833,837 - 39,876,274 (+)NCBICHM1_1
Samd4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,689,413 - 83,728,652 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl185,324,043 - 85,362,241 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0185,324,017 - 85,362,266 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0186,543,900 - 86,577,571 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,506,971 - 83,531,789 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,585,834 - 83,609,901 (-)NCBI
Celera178,085,681 - 78,110,098 (-)NCBICelera
Cytogenetic Map1q21NCBI
Samd4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955468172,352 - 199,230 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955468172,331 - 199,230 (-)NCBIChiLan1.0ChiLan1.0
SAMD4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11944,990,081 - 45,031,673 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1945,002,848 - 45,031,649 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01936,440,769 - 36,483,953 (+)NCBIMhudiblu_PPA_v0panPan3
SAMD4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11113,828,432 - 113,857,336 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1113,828,447 - 113,857,314 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1113,231,809 - 113,274,282 (-)NCBI
ROS_Cfam_1.01114,429,074 - 114,471,549 (-)NCBI
UMICH_Zoey_3.11113,987,790 - 114,030,223 (-)NCBI
UNSW_CanFamBas_1.01113,620,568 - 113,663,020 (-)NCBI
UU_Cfam_GSD_1.01114,615,665 - 114,658,139 (-)NCBI
Samd4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934913,779,811 - 13,808,124 (+)NCBI
SpeTri2.0NW_0049366612,208,852 - 2,234,660 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl648,002,712 - 48,046,561 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1648,002,726 - 48,046,563 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214143,698,232 - 143,724,853 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1633,949,045 - 33,990,410 (+)NCBI
ChlSab1.1 Ensembl633,963,231 - 33,988,246 (+)Ensembl
Vero_WHO_p1.0NW_02366607311,969,284 - 12,010,771 (+)NCBI
Samd4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479412,677,695 - 12,724,595 (+)NCBI

Position Markers
BG376329  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38728,400,485 - 28,400,676UniSTSGRCm38
MGSCv37729,185,504 - 29,185,695UniSTSGRCm37
Celera722,962,074 - 22,962,265UniSTS
Cytogenetic Map7A3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301572Sluc30_msusceptibility to lung cancer 30 (mouse)Not determined7269777136697919Mouse
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7346321287493512Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360000072900000Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76500000133900000Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined71028944244289559Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71060637344606511Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71278145246781452Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71278145246781452Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1333306047333196Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71343577947435779Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71360000047700000Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71690336849509583Mouse
1301041Prnr2_mprion resistance 2 (mouse)Not determined71899486940024609Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718994869119886157Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719413473142366067Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71958059053580679Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined72014282554142942Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72302446357024609Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72323914857239292Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72341710757417107Mouse
1301969Lbw5_mlupus NZB x NZW 5 (mouse)Not determined72719819161202351Mouse
7394747asp3_maudiogenic seizure prone 3 (mouse)Not determined72760637337142942Mouse
12790989Tgl6_mtriglyceride 6 (mouse)72789112561891125Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:922
Count of miRNA genes:494
Interacting mature miRNAs:560
Transcripts:ENSMUST00000040531
Prediction methods:Miranda, Rnahybrid
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000040531   ⟹   ENSMUSP00000040486
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl728,399,549 - 28,598,144 (-)Ensembl
RefSeq Acc Id: ENSMUST00000207766   ⟹   ENSMUSP00000146984
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl728,401,461 - 28,436,227 (-)Ensembl
RefSeq Acc Id: ENSMUST00000208126   ⟹   ENSMUSP00000146657
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl728,401,297 - 28,404,031 (-)Ensembl
RefSeq Acc Id: ENSMUST00000208199   ⟹   ENSMUSP00000147037
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl728,399,522 - 28,436,191 (-)Ensembl
RefSeq Acc Id: ENSMUST00000208676
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl728,407,298 - 28,413,907 (-)Ensembl
RefSeq Acc Id: NM_175021   ⟹   NP_778186
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39728,098,947 - 28,135,616 (-)NCBI
GRCm38728,399,522 - 28,436,191 (-)ENTREZGENE
MGSCv37729,184,541 - 29,221,210 (-)RGD
Celera722,961,111 - 22,997,787 (-)RGD
cM Map7 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_778186 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL24136 (Get FASTA)   NCBI Sequence Viewer  
  EDL24137 (Get FASTA)   NCBI Sequence Viewer  
  Q80XS6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_778186   ⟸   NM_175021
- UniProtKB: G5E8A7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000040486   ⟸   ENSMUST00000040531
RefSeq Acc Id: ENSMUSP00000146657   ⟸   ENSMUST00000208126
RefSeq Acc Id: ENSMUSP00000147037   ⟸   ENSMUST00000208199
RefSeq Acc Id: ENSMUSP00000146984   ⟸   ENSMUST00000207766
Protein Domains
SAM

Promoters
RGD ID:6892456
Promoter ID:EPDNEW_M9679
Type:initiation region
Name:Samd4b_1
Description:Mus musculus sterile alpha motif domain containing 4B , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38728,436,288 - 28,436,348EPDNEW
RGD ID:6848202
Promoter ID:MM_ACW:44027
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_4Hour,   Brain
Transcripts:SAMD4B.BSEP07
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36729,191,319 - 29,191,819 (-)MPROMDB
RGD ID:6848201
Promoter ID:MM_ACW:44028
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_2Hour
Transcripts:SAMD4B.CSEP07-UNSPLICED,   SAMD4B.DSEP07
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36729,198,946 - 29,199,446 (-)MPROMDB
RGD ID:6841974
Promoter ID:MM_KWN:49642
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_2Hour
Transcripts:ENSMUST00000040531
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36729,208,496 - 29,208,996 (-)MPROMDB
RGD ID:6841245
Promoter ID:MM_KWN:49643
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:AK007003_1700085B13RIK,   ENSMUST00000108289,   NM_022024,   NM_175021
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36729,221,556 - 29,222,187 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2448542 AgrOrtholog
Ensembl Genes ENSMUSG00000109336 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000040486 UniProtKB/TrEMBL
  ENSMUSP00000146657 UniProtKB/TrEMBL
  ENSMUSP00000146984 UniProtKB/TrEMBL
  ENSMUSP00000147037 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000040531 UniProtKB/TrEMBL
  ENSMUST00000207766 UniProtKB/TrEMBL
  ENSMUST00000208126 UniProtKB/TrEMBL
  ENSMUST00000208199 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Smaug_SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:233033 UniProtKB/TrEMBL
MGD MGI:2448542 ENTREZGENE
NCBI Gene 233033 ENTREZGENE
Pfam SAM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Samd4b PhenoGen
SMART SAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140LI35_MOUSE UniProtKB/TrEMBL
  A0A140LIW4_MOUSE UniProtKB/TrEMBL
  G5E8A7 ENTREZGENE, UniProtKB/TrEMBL
  Q80XS6 ENTREZGENE, UniProtKB/Swiss-Prot