Msantd4 (Myb/SANT DNA binding domain containing 4 with coiled-coils) - Rat Genome Database

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Gene: Msantd4 (Myb/SANT DNA binding domain containing 4 with coiled-coils) Rattus norvegicus
Analyze
Symbol: Msantd4
Name: Myb/SANT DNA binding domain containing 4 with coiled-coils
RGD ID: 1565380
Description: Predicted to be located in nucleus. Orthologous to human MSANTD4 (Myb/SANT DNA binding domain containing 4 with coiled-coils); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; gentamycin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: coiled-coil domain-containing protein KIAA1826 homolog; hypothetical protein LOC500941; MGC105560; Myb/SANT-like DNA-binding domain containing 4 with coiled-coils; myb/SANT-like DNA-binding domain-containing protein 4; similar to Hypothetical protein BC014729
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
GRCr889,801,921 - 9,812,529 (+)NCBIGRCr8
mRatBN7.281,516,979 - 1,527,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl81,516,979 - 1,527,587 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx85,504,431 - 5,515,046 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.083,802,169 - 3,812,784 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.081,748,297 - 1,758,904 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.081,503,018 - 1,513,626 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl81,502,877 - 1,513,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.081,497,145 - 1,507,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48910,994 - 921,602 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera81,399,976 - 1,410,584 (+)NCBICelera
Cytogenetic Map8q11NCBI
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

Cellular Component
nucleus  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Msantd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr889,801,921 - 9,812,529 (+)NCBIGRCr8
mRatBN7.281,516,979 - 1,527,587 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl81,516,979 - 1,527,587 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx85,504,431 - 5,515,046 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.083,802,169 - 3,812,784 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.081,748,297 - 1,758,904 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.081,503,018 - 1,513,626 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl81,502,877 - 1,513,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.081,497,145 - 1,507,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48910,994 - 921,602 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera81,399,976 - 1,410,584 (+)NCBICelera
Cytogenetic Map8q11NCBI
MSANTD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811106,007,899 - 106,022,287 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11105,995,623 - 106,022,403 (-)EnsemblGRCh38hg38GRCh38
GRCh3711105,878,626 - 105,893,014 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611105,383,839 - 105,398,164 (-)NCBINCBI36Build 36hg18NCBI36
Celera11103,042,885 - 103,057,210 (-)NCBICelera
Cytogenetic Map11q22.3NCBI
HuRef11101,809,702 - 101,824,027 (-)NCBIHuRef
CHM1_111105,761,601 - 105,775,928 (-)NCBICHM1_1
T2T-CHM13v2.011106,012,491 - 106,026,880 (-)NCBIT2T-CHM13v2.0
Msantd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3994,376,552 - 4,386,890 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl94,376,562 - 4,386,870 (+)EnsemblGRCm39 Ensembl
GRCm3894,376,552 - 4,386,890 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl94,376,562 - 4,386,870 (+)EnsemblGRCm38mm10GRCm38
MGSCv3794,383,535 - 4,386,870 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3694,376,612 - 4,386,870 (+)NCBIMGSCv36mm8
Celera3118,318,018 - 118,321,353 (-)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Msantd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554128,652,193 - 8,666,347 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554128,654,182 - 8,666,254 (-)NCBIChiLan1.0ChiLan1.0
MSANTD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29106,752,481 - 106,770,678 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111107,850,736 - 107,865,242 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v011100,899,541 - 100,913,926 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111104,383,403 - 104,397,767 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11104,383,412 - 104,397,702 (-)Ensemblpanpan1.1panPan2
MSANTD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1526,251,313 - 26,257,984 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl526,251,180 - 26,256,237 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha526,176,538 - 26,183,204 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0526,279,946 - 26,286,603 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl526,280,594 - 26,284,853 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1526,330,319 - 26,336,996 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0526,215,732 - 26,222,402 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0526,365,353 - 26,372,025 (+)NCBIUU_Cfam_GSD_1.0
Msantd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494789,132,069 - 89,145,062 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365512,391,565 - 2,404,389 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365512,391,518 - 2,404,421 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSANTD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl935,830,837 - 35,862,114 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1935,828,697 - 35,839,579 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2939,846,084 - 39,875,760 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSANTD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1197,405,837 - 97,420,276 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl197,407,462 - 97,420,124 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604328,461,174 - 28,475,650 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msantd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624784804,925 - 817,122 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624784805,556 - 817,303 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Msantd4
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:904
Count of miRNA genes:319
Interacting mature miRNAs:422
Transcripts:ENSRNOT00000034482
Prediction methods:Microtar, Miranda, 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
71120Niddm21Non-insulin dependent diabetes mellitus QTL 213.73blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)813402289Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat

Markers in Region
RH131202  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.281,527,275 - 1,527,465 (+)MAPPERmRatBN7.2
Rnor_6.081,513,315 - 1,513,504NCBIRnor6.0
Rnor_5.081,507,442 - 1,507,631UniSTSRnor5.0
RGSC_v3.48921,291 - 921,480UniSTSRGSC3.4
Celera81,410,273 - 1,410,462UniSTS
Cytogenetic Map8q11UniSTS


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 21 141 195 115 65 115 36 45 250 115 106 57 24
Low 32 32 32 39
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000034482   ⟹   ENSRNOP00000030251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl81,516,979 - 1,527,587 (+)Ensembl
Rnor_6.0 Ensembl81,502,877 - 1,513,603 (+)Ensembl
RefSeq Acc Id: NM_001024357   ⟹   NP_001019528
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr889,801,921 - 9,812,529 (+)NCBI
mRatBN7.281,516,979 - 1,527,587 (+)NCBI
Rnor_6.081,503,018 - 1,513,626 (+)NCBI
Rnor_5.081,497,145 - 1,507,753 (+)NCBI
RGSC_v3.48910,994 - 921,602 (+)RGD
Celera81,399,976 - 1,410,584 (+)RGD
Sequence:
RefSeq Acc Id: XM_063265957   ⟹   XP_063122027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr889,801,952 - 9,812,511 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001019528 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122027 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH96000 (Get FASTA)   NCBI Sequence Viewer  
  EDL85229 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030251.3
  ENSRNOP00055007556
  ENSRNOP00060007937
  ENSRNOP00060021497
  ENSRNOP00065002461
GenBank Protein Q501L3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001019528   ⟸   NM_001024357
- UniProtKB: Q501L3 (UniProtKB/Swiss-Prot),   A6KQJ5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000030251   ⟸   ENSRNOT00000034482
RefSeq Acc Id: XP_063122027   ⟸   XM_063265957
- Peptide Label: isoform X1
- UniProtKB: Q501L3 (UniProtKB/Swiss-Prot),   A6KQJ5 (UniProtKB/TrEMBL)
Protein Domains
Myb-like   Myb/SANT-like DNA-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q501L3-F1-model_v2 AlphaFold Q501L3 1-345 view protein structure

Transcriptome

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

Promoters
RGD ID:13695724
Promoter ID:EPDNEW_R6249
Type:initiation region
Name:Msantd4_1
Description:Myb/SANT DNA binding domain containing 4 with coiled-coils
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_6.081,503,011 - 1,503,071EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565380 AgrOrtholog
BioCyc Gene G2FUF-31835 BioCyc
Ensembl Genes ENSRNOG00000022245 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055006057 UniProtKB/Swiss-Prot
  ENSRNOG00060006540 UniProtKB/Swiss-Prot
  ENSRNOG00060015659 UniProtKB/Swiss-Prot
  ENSRNOG00065002656 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000034482.5 UniProtKB/Swiss-Prot
  ENSRNOT00055009797 UniProtKB/Swiss-Prot
  ENSRNOT00060010707 UniProtKB/Swiss-Prot
  ENSRNOT00060026822 UniProtKB/Swiss-Prot
  ENSRNOT00065003568 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7308051 IMAGE-MGC_LOAD
InterPro MSANTD4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Myb_DNA-bind_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500941 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105560 IMAGE-MGC_LOAD
NCBI Gene 500941 ENTREZGENE
PANTHER MYB/SANT-LIKE DNA-BINDING DOMAIN-CONTAINING PROTEIN 4 UniProtKB/Swiss-Prot
  MYB/SANT-LIKE DNA-BINDING DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  MYB/SANT-LIKE DNA-BINDING DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PTHR21732 UniProtKB/Swiss-Prot
Pfam Myb_DNA-bind_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Msantd4 PhenoGen
RatGTEx ENSRNOG00000022245 RatGTEx
  ENSRNOG00055006057 RatGTEx
  ENSRNOG00060006540 RatGTEx
  ENSRNOG00060015659 RatGTEx
  ENSRNOG00065002656 RatGTEx
UniProt A6KQJ5 ENTREZGENE, UniProtKB/TrEMBL
  MSD4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Msantd4  Myb/SANT DNA binding domain containing 4 with coiled-coils  Msantd4  Myb/SANT-like DNA-binding domain containing 4 with coiled-coils  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-05 Msantd4  Myb/SANT-like DNA-binding domain containing 4 with coiled-coils  MGC105560  similar to Hypothetical protein BC014729  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 MGC105560  similar to Hypothetical protein BC014729      Symbol and Name status set to provisional 70820 PROVISIONAL