Ascl4 (achaete-scute family bHLH transcription factor 4) - Rat Genome Database

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Gene: Ascl4 (achaete-scute family bHLH transcription factor 4) Rattus norvegicus
Analyze
Symbol: Ascl4
Name: achaete-scute family bHLH transcription factor 4
RGD ID: 1307533
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of RNA polymerase II transcription regulator complex. Orthologous to human ASCL4 (achaete-scute family bHLH transcription factor 4); INTERACTS WITH bisphenol A; ferrostatin-1; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: achaete-scute complex homolog 4; achaete-scute complex homolog 4 (Drosophila); achaete-scute complex-like 4; achaete-scute complex-like 4 (Drosophila); achaete-scute homolog 4; LOC299687
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8719,828,710 - 19,830,952 (-)NCBIGRCr8
mRatBN7.2717,940,972 - 17,943,215 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl717,941,709 - 17,942,146 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx719,903,142 - 19,905,382 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0722,066,431 - 22,068,687 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0721,842,785 - 21,845,025 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0723,946,974 - 23,949,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,947,765 - 23,948,202 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,096,570 - 24,099,125 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,079,914 - 20,080,351 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1720,093,984 - 20,094,989 (-)NCBI
Celera715,173,149 - 15,175,774 (-)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ascl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8719,828,710 - 19,830,952 (-)NCBIGRCr8
mRatBN7.2717,940,972 - 17,943,215 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl717,941,709 - 17,942,146 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx719,903,142 - 19,905,382 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0722,066,431 - 22,068,687 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0721,842,785 - 21,845,025 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0723,946,974 - 23,949,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,947,765 - 23,948,202 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,096,570 - 24,099,125 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,079,914 - 20,080,351 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1720,093,984 - 20,094,989 (-)NCBI
Celera715,173,149 - 15,175,774 (-)NCBICelera
Cytogenetic Map7q13NCBI
ASCL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812107,774,704 - 107,776,644 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12107,774,704 - 107,776,644 (+)EnsemblGRCh38hg38GRCh38
GRCh3712108,168,481 - 108,170,421 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612106,692,292 - 106,694,545 (+)NCBINCBI36Build 36hg18NCBI36
Build 3412106,670,628 - 106,672,882NCBI
Celera12107,833,712 - 107,835,971 (+)NCBICelera
Cytogenetic Map12q23.3NCBI
HuRef12105,228,648 - 105,230,907 (+)NCBIHuRef
CHM1_112108,134,114 - 108,136,373 (+)NCBICHM1_1
T2T-CHM13v2.012107,738,195 - 107,740,135 (+)NCBIT2T-CHM13v2.0
Ascl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391085,763,266 - 85,765,513 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1085,763,545 - 85,782,070 (+)EnsemblGRCm39 Ensembl
GRCm381085,927,402 - 85,929,649 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1085,927,681 - 85,946,206 (+)EnsemblGRCm38mm10GRCm38
MGSCv371085,391,236 - 85,392,392 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361085,358,290 - 85,359,167 (+)NCBIMGSCv36mm8
Celera1087,903,088 - 87,904,244 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1041.8NCBI
ASCL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210115,825,186 - 115,835,323 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112115,821,599 - 115,831,720 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012105,344,528 - 105,346,779 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112108,743,237 - 108,743,756 (+)NCBIpanpan1.1PanPan1.1panPan2
ASCL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11031,053,716 - 31,056,234 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1031,053,744 - 31,054,265 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1031,036,584 - 31,037,754 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01031,896,305 - 31,897,475 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11031,635,850 - 31,637,020 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01031,924,911 - 31,926,075 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01032,111,507 - 32,112,676 (-)NCBIUU_Cfam_GSD_1.0
Ascl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494514,368,536 - 14,370,113 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364927,379,349 - 7,379,918 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364927,378,982 - 7,379,918 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ASCL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl512,623,691 - 12,624,209 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1512,623,691 - 12,625,193 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2512,409,905 - 12,412,454 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ASCL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111102,993,754 - 103,038,173 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11102,994,906 - 102,995,424 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037142,077,344 - 142,080,344 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Ascl4
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:83
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000044252
Prediction methods:Microtar, Miranda, 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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 3 2 12 21 17
Below cutoff 15 12 7 12 2 2 39 12 18 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044252   ⟹   ENSRNOP00000051020
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,941,709 - 17,942,146 (-)Ensembl
Rnor_6.0 Ensembl723,947,765 - 23,948,202 (-)Ensembl
RefSeq Acc Id: NM_001399717   ⟹   NP_001386646
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8719,828,710 - 19,830,952 (-)NCBI
mRatBN7.2717,940,972 - 17,943,215 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386646 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000051020
  ENSRNOP00000051020.2
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000051020   ⟸   ENSRNOT00000044252
RefSeq Acc Id: NP_001386646   ⟸   NM_001399717
- UniProtKB: D3ZS54 (UniProtKB/TrEMBL)
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZS54-F1-model_v2 AlphaFold D3ZS54 1-145 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:1307533 AgrOrtholog
BioCyc Gene G2FUF-34637 BioCyc
Ensembl Genes ENSRNOG00000031493 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044252 ENTREZGENE
  ENSRNOT00000044252.3 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 299687 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST UniProtKB/TrEMBL
  FACTOR IN THE GERMLINE ALPHA UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Ascl4 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031493 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt D3ZS54 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-11 Ascl4  achaete-scute family bHLH transcription factor 4  Ascl4  achaete-scute complex homolog 4 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Ascl4  achaete-scute complex homolog 4 (Drosophila)  Ascl4_predicted  achaete-scute complex-like 4 (Drosophila) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Ascl4_predicted  achaete-scute complex-like 4 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED