Ascl1 (achaete-scute family bHLH transcription factor 1) - Rat Genome Database

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Gene: Ascl1 (achaete-scute family bHLH transcription factor 1) Rattus norvegicus
Analyze
Symbol: Ascl1
Name: achaete-scute family bHLH transcription factor 1
RGD ID: 71010
Description: Exhibits double-stranded DNA binding activity and identical protein binding activity. Involved in several processes, including cellular response to magnetism; regulation of neuron differentiation; and response to epidermal growth factor. Predicted to localize to RNA polymerase II transcription regulator complex and neuronal cell body. Biomarker of status epilepticus. Human ortholog(s) of this gene implicated in congenital central hypoventilation syndrome. Orthologous to human ASCL1 (achaete-scute family bHLH transcription factor 1); INTERACTS WITH (S)-nicotine; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: achaete-scute complex (Drosophila) homolog-like 1; achaete-scute complex homolog 1; achaete-scute complex homolog 1 (Drosophila); achaete-scute complex homolog-like 1; achaete-scute complex homolog-like 1 (Drosophila); achaete-scute homolog 1; Mash1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2721,904,153 - 21,906,003 (-)NCBI
Rnor_6.0 Ensembl728,038,662 - 28,040,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0728,038,662 - 28,040,504 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0728,152,425 - 28,154,275 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4724,145,578 - 24,168,494 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1724,165,848 - 24,167,679 (-)NCBI
Celera719,079,344 - 19,081,186 (-)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process
adrenal chromaffin cell differentiation  (ISO)
carotid body glomus cell differentiation  (ISO)
cell differentiation  (ISO)
cell maturation  (ISO)
cellular response to magnetism  (IEP)
central nervous system neuron development  (ISO)
cerebral cortex development  (ISO)
cerebral cortex GABAergic interneuron differentiation  (ISO)
commitment of neuronal cell to specific neuron type in forebrain  (ISO)
forebrain neuron differentiation  (IDA)
generation of neurons  (ISO)
glial cell differentiation  (ISO)
heart development  (IEP)
lung neuroendocrine cell differentiation  (ISO)
musculoskeletal movement, spinal reflex action  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of neuron differentiation  (IDA,ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
nervous system development  (IDA,ISO)
neuroblast fate determination  (ISO)
neuroblast proliferation  (ISO)
neurogenesis  (ISO)
neuron development  (ISO,ISS)
neuron differentiation  (IBA,ISO)
neuron fate commitment  (ISO,ISS)
neuron fate specification  (ISO,ISS)
neuron migration  (ISO)
noradrenergic neuron development  (ISO,ISS)
noradrenergic neuron fate commitment  (ISO)
Notch signaling pathway  (ISO)
olfactory pit development  (ISO)
oligodendrocyte cell fate commitment  (ISO)
oligodendrocyte development  (ISO)
oligodendrocyte differentiation  (ISO)
pattern specification process  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of neural precursor cell proliferation  (ISO)
positive regulation of neurogenesis  (ISO)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of neuron differentiation  (IDA)
positive regulation of Notch signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of cell population proliferation  (ISO)
regulation of epithelial cell differentiation  (ISO)
regulation of gene expression  (ISO,ISS)
regulation of mitotic cell cycle  (ISO)
regulation of neurogenesis  (IBA,ISO)
regulation of Notch signaling pathway  (ISO)
regulation of timing of subpallium neuron differentiation  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
response to epidermal growth factor  (IEP)
response to folic acid  (IEP)
response to lithium ion  (IEP)
response to retinoic acid  (IEP,ISO)
sensory organ development  (IBA)
spinal cord association neuron differentiation  (ISO)
spinal cord oligodendrocyte cell differentiation  (ISO)
spinal cord oligodendrocyte cell fate specification  (ISO)
stomach neuroendocrine cell differentiation  (ISO)
subpallium neuron fate commitment  (ISO)
sympathetic ganglion development  (ISO,ISS)
ventral spinal cord interneuron fate commitment  (ISO,ISS)
vestibular nucleus development  (ISO)

Cellular Component

References

References - curated
1. Ahmad I, etal., Dev Biol. 1998 Feb 1;194(1):86-98.
2. Asson-Batres MA, etal., J Neurobiol 2003 Mar;54(4):539-54.
3. Chen J, etal., Neuroscience. 2006 Aug 25;141(2):737-44. Epub 2006 May 30.
4. Elliott RC, etal., Neuroscience. 2001;106(1):79-88.
5. Farah MH, etal., Development. 2000 Feb;127(4):693-702.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Guillemot F, etal., Cell 1993 Nov 5;75(3):463-76.
9. Jo AY, etal., Exp Cell Res. 2007 Nov 15;313(19):4066-81. Epub 2007 Sep 8.
10. Johnson JE, etal., Nature 1990 Aug 30;346(6287):858-61.
11. K-unne AG, etal., Biochemistry. 1998 Mar 24;37(12):4217-23.
12. Kappes A, etal., Surgery. 2007 Feb;141(2):161-5; discussion 165.
13. Kury P, etal., J Neurosci 2002 Sep 1;22(17):7586-95.
14. Lo L, etal., Development 2002 Apr;129(7):1553-67.
15. MGD Curation, June 12, 2002
16. MGD data from the GO Consortium
17. Nakamichi N, etal., J Neurosci Res. 2009 Aug 15;87(11):2406-17.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. OMIM Disease Annotation Pipeline
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Shoba T, etal., Neurosci Lett 2002 Feb 1;318(3):129-32.
24. Zhang X, etal., J Nutr Sci Vitaminol (Tokyo). 2008 Oct;54(5):353-6.
Additional References at PubMed
PMID:1576967   PMID:8845150   PMID:8900141   PMID:9108377   PMID:9126746   PMID:9876181   PMID:10903890   PMID:10952889   PMID:11032813   PMID:11073877   PMID:11133151   PMID:11736660  
PMID:11940670   PMID:12000752   PMID:12050665   PMID:12361965   PMID:12397111   PMID:12629181   PMID:12858003   PMID:12885554   PMID:14532329   PMID:15065125   PMID:15071116   PMID:15133515  
PMID:15169849   PMID:15854743   PMID:15878769   PMID:15930101   PMID:15976074   PMID:16020526   PMID:16160079   PMID:16469766   PMID:16715081   PMID:16723737   PMID:16766700   PMID:17141158  
PMID:17488716   PMID:17507989   PMID:17678855   PMID:17727826   PMID:18094025   PMID:18173746   PMID:18184563   PMID:18287202   PMID:18311112   PMID:18781144   PMID:19008346   PMID:19097999  
PMID:19191219   PMID:19399893   PMID:19793887   PMID:19796622   PMID:20144606   PMID:20599619   PMID:21536733   PMID:22583763   PMID:22991444   PMID:23284756   PMID:23434913   PMID:23616538  
PMID:23639443   PMID:23792135   PMID:24144723   PMID:24243019   PMID:25124043   PMID:25751153   PMID:26437572   PMID:28276447   PMID:31317490   PMID:33631250  


Genomics

Comparative Map Data
Ascl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2721,904,153 - 21,906,003 (-)NCBI
Rnor_6.0 Ensembl728,038,662 - 28,040,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0728,038,662 - 28,040,504 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0728,152,425 - 28,154,275 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4724,145,578 - 24,168,494 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1724,165,848 - 24,167,679 (-)NCBI
Celera719,079,344 - 19,081,186 (-)NCBICelera
Cytogenetic Map7q13NCBI
ASCL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12102,957,674 - 102,960,513 (+)EnsemblGRCh38hg38GRCh38
GRCh3812102,957,674 - 102,960,513 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712103,351,452 - 103,354,291 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612101,875,594 - 101,878,421 (+)NCBINCBI36hg18NCBI36
Build 3412101,853,930 - 101,856,754NCBI
Celera12103,015,725 - 103,018,566 (+)NCBI
Cytogenetic Map12q23.2NCBI
HuRef12100,410,703 - 100,413,544 (+)NCBIHuRef
CHM1_112103,318,246 - 103,321,086 (+)NCBICHM1_1
Ascl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391087,326,681 - 87,329,522 (-)NCBIGRCm39mm39
GRCm39 Ensembl1087,326,681 - 87,329,522 (-)Ensembl
GRCm381087,490,819 - 87,493,660 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1087,490,819 - 87,493,660 (-)EnsemblGRCm38mm10GRCm38
MGSCv371086,953,786 - 86,956,405 (-)NCBIGRCm37mm9NCBIm37
MGSCv361086,920,621 - 86,922,980 (-)NCBImm8
Celera1089,464,389 - 89,467,010 (-)NCBICelera
Cytogenetic Map10C1NCBI
Ascl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540537,941,243 - 37,943,641 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540537,941,243 - 37,943,641 (+)NCBIChiLan1.0ChiLan1.0
ASCL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112103,931,707 - 103,934,554 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12103,932,302 - 103,932,999 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012100,536,895 - 100,539,737 (+)NCBIMhudiblu_PPA_v0panPan3
ASCL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11541,694,021 - 41,696,933 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1541,694,269 - 41,695,391 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1542,062,179 - 42,065,075 (+)NCBI
ROS_Cfam_1.01542,349,900 - 42,352,808 (+)NCBI
UMICH_Zoey_3.11541,619,328 - 41,622,224 (+)NCBI
UNSW_CanFamBas_1.01541,717,251 - 41,720,147 (+)NCBI
UU_Cfam_GSD_1.01541,986,771 - 41,989,679 (+)NCBI
Ascl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494518,304,396 - 18,306,779 (-)NCBI
SpeTri2.0NW_00493649211,315,929 - 11,317,166 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ASCL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1581,357,431 - 81,360,335 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ASCL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11198,182,213 - 98,185,057 (+)NCBI
ChlSab1.1 Ensembl1198,182,787 - 98,183,506 (+)Ensembl
Vero_WHO_p1.0NW_023666037146,827,687 - 146,830,550 (-)NCBI
Ascl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247505,487,046 - 5,489,399 (-)NCBI

Position Markers
Ascl1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2721,904,669 - 21,905,151 (+)MAPPER
Rnor_6.0728,039,179 - 28,039,660NCBIRnor6.0
Rnor_5.0728,152,942 - 28,153,423UniSTSRnor5.0
RGSC_v3.4724,146,095 - 24,146,576UniSTSRGSC3.4
Celera719,079,861 - 19,080,342UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (Rnor_6.0)
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)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72417533732258115Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72473868040433335Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72536563357064364Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72536563357064364Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72650888736346595Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:41
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000005674
Prediction methods: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.


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 4 4 4 45 4
Low 2 22 10 8 10 29 14
Below cutoff 3 6 8 4 1 4 3 4 4 9 11 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005674   ⟹   ENSRNOP00000005674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl728,038,662 - 28,040,510 (-)Ensembl
RefSeq Acc Id: NM_022384   ⟹   NP_071779
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2721,904,153 - 21,906,003 (-)NCBI
Rnor_6.0728,038,662 - 28,040,504 (-)NCBI
Rnor_5.0728,152,425 - 28,154,275 (-)NCBI
RGSC_v3.4724,145,578 - 24,168,494 (-)RGD
Celera719,079,344 - 19,081,186 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_071779 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA37760 (Get FASTA)   NCBI Sequence Viewer  
  EDM17037 (Get FASTA)   NCBI Sequence Viewer  
  P19359 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071779   ⟸   NM_022384
- UniProtKB: P19359 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005674   ⟸   ENSRNOT00000005674
Protein Domains
bHLH

Transcriptome

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

Promoters
RGD ID:13695118
Promoter ID:EPDNEW_R5643
Type:single initiation site
Name:Ascl1_1
Description:achaete-scute family bHLH transcription factor 1
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_6.0728,040,491 - 28,040,551EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71010 AgrOrtholog
Ensembl Genes ENSRNOG00000004294 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000005674 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005674 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot
InterPro bHLH_dom UniProtKB/Swiss-Prot
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot
  MASH1/Ascl1a-like UniProtKB/Swiss-Prot
KEGG Report rno:64186 UniProtKB/Swiss-Prot
NCBI Gene 64186 ENTREZGENE
PANTHER PTHR13935 UniProtKB/Swiss-Prot
Pfam HLH UniProtKB/Swiss-Prot
PhenoGen Ascl1 PhenoGen
PROSITE BHLH UniProtKB/Swiss-Prot
SMART HLH UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot
UniProt ASCL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-11 Ascl1  achaete-scute family bHLH transcription factor 1  Ascl1  achaete-scute complex homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Ascl1  achaete-scute complex homolog 1 (Drosophila)  Ascl1  achaete-scute complex homolog-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Ascl1  achaete-scute complex homolog-like 1 (Drosophila)      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference