Lyl1 (LYL1, basic helix-loop-helix family member) - Rat Genome Database

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Gene: Lyl1 (LYL1, basic helix-loop-helix family member) Rattus norvegicus
Analyze
Symbol: Lyl1
Name: LYL1, basic helix-loop-helix family member
RGD ID: 1359244
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in blood vessel maturation; hemopoiesis; and regulation of DNA-templated transcription. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in T-cell acute lymphoblastic leukemia. Orthologous to human LYL1 (LYL1 basic helix-loop-helix family member); INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: lymphoblastic leukemia associated hematopoiesis regulator 1; lymphoblastic leukemia derived sequence 1; lymphoblastic leukemia-derived sequence 1; MGC93688; protein lyl-1; protein lyl-1-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81940,356,967 - 40,359,834 (-)NCBIGRCr8
mRatBN7.21923,452,140 - 23,455,007 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1923,452,140 - 23,455,007 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1930,274,992 - 30,277,859 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01930,929,369 - 30,932,236 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01933,152,064 - 33,154,931 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01925,815,207 - 25,818,074 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,815,207 - 25,818,074 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,790,826 - 36,793,693 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,115,234 - 25,118,100 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11925,120,059 - 25,122,926 (-)NCBI
Celera1923,005,834 - 23,008,676 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IEA)

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. Structure, chromosome mapping, and expression of the mouse Lyl-1 gene. Kuo SS, etal., Oncogene 1991 Jun;6(6):961-8.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. 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.
Additional References at PubMed
PMID:10023675   PMID:16514064   PMID:18160048   PMID:20418284  


Genomics

Comparative Map Data
Lyl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81940,356,967 - 40,359,834 (-)NCBIGRCr8
mRatBN7.21923,452,140 - 23,455,007 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1923,452,140 - 23,455,007 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1930,274,992 - 30,277,859 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01930,929,369 - 30,932,236 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01933,152,064 - 33,154,931 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01925,815,207 - 25,818,074 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,815,207 - 25,818,074 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,790,826 - 36,793,693 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,115,234 - 25,118,100 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11925,120,059 - 25,122,926 (-)NCBI
Celera1923,005,834 - 23,008,676 (-)NCBICelera
Cytogenetic Map19q11NCBI
LYL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381913,099,033 - 13,102,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1913,099,033 - 13,103,161 (-)EnsemblGRCh38hg38GRCh38
GRCh371913,209,847 - 13,213,672 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,070,847 - 13,074,681 (-)NCBINCBI36Build 36hg18NCBI36
Build 341913,070,847 - 13,074,681NCBI
Celera1913,100,251 - 13,104,085 (-)NCBICelera
Cytogenetic Map19p13.13NCBI
HuRef1912,782,481 - 12,786,613 (-)NCBIHuRef
CHM1_11913,210,856 - 13,214,988 (-)NCBICHM1_1
T2T-CHM13v2.01913,224,247 - 13,228,072 (-)NCBIT2T-CHM13v2.0
Lyl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,428,051 - 85,432,876 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl885,428,078 - 85,431,569 (+)EnsemblGRCm39 Ensembl
GRCm38884,701,423 - 84,704,716 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,701,449 - 84,704,940 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,225,356 - 87,228,615 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36887,591,649 - 87,594,797 (+)NCBIMGSCv36mm8
Celera889,001,525 - 89,004,783 (+)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.02NCBI
Lyl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,121,808 - 32,124,730 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,121,808 - 32,124,730 (-)NCBIChiLan1.0ChiLan1.0
LYL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22018,027,082 - 18,032,961 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11917,026,337 - 17,032,154 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01912,660,548 - 12,664,513 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11913,404,544 - 13,415,231 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,407,596 - 13,409,309 (-)Ensemblpanpan1.1panPan2
LYL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,109,358 - 49,113,911 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,982,650 - 48,986,414 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02049,628,499 - 49,630,905 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2049,628,825 - 49,630,609 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12048,838,699 - 48,842,459 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02049,265,053 - 49,268,813 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02049,507,463 - 49,511,227 (+)NCBIUU_Cfam_GSD_1.0
Lyl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,213,865 - 208,219,664 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366592,135,270 - 2,140,676 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366592,135,253 - 2,140,849 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,952,519 - 65,955,011 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,950,608 - 65,956,423 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,314,840 - 66,320,282 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LYL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,778,634 - 11,785,474 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl611,780,766 - 11,782,618 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660747,998,417 - 8,005,282 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lyl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624901645,924 - 649,100 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624901645,263 - 648,550 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lyl1
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:265
Count of miRNA genes:177
Interacting mature miRNAs:202
Transcripts:ENSRNOT00000003980
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
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat


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 2 16 22 22 11 22 14
Low 1 27 35 19 8 19 8 11 74 35 27 11 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000003980   ⟹   ENSRNOP00000003980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1923,452,140 - 23,455,007 (-)Ensembl
Rnor_6.0 Ensembl1925,815,207 - 25,818,074 (+)Ensembl
RefSeq Acc Id: NM_001007677   ⟹   NP_001007678
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81940,356,967 - 40,359,834 (-)NCBI
mRatBN7.21923,452,140 - 23,455,007 (-)NCBI
Rnor_6.01925,815,207 - 25,818,074 (+)NCBI
Rnor_5.01936,790,826 - 36,793,693 (+)NCBI
RGSC_v3.41925,115,234 - 25,118,100 (-)RGD
Celera1923,005,834 - 23,008,676 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001007678 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81864 (Get FASTA)   NCBI Sequence Viewer  
  EDL92206 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003980
  ENSRNOP00000003980.2
  ENSRNOP00055010571
  ENSRNOP00060017305
  ENSRNOP00065011371
GenBank Protein Q66HH3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001007678   ⟸   NM_001007677
- UniProtKB: Q66HH3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003980   ⟸   ENSRNOT00000003980
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HH3-F1-model_v2 AlphaFold Q66HH3 1-278 view protein structure

Transcriptome

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

Promoters
RGD ID:13701022
Promoter ID:EPDNEW_R11546
Type:initiation region
Name:Lyl1_1
Description:LYL1, basic helix-loop-helix family member
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_6.01925,815,190 - 25,815,250EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359244 AgrOrtholog
BioCyc Gene G2FUF-6112 BioCyc
Ensembl Genes ENSRNOG00000002950 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055007859 UniProtKB/Swiss-Prot
  ENSRNOG00060012865 UniProtKB/Swiss-Prot
  ENSRNOG00065009482 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003980 ENTREZGENE
  ENSRNOT00000003980.4 UniProtKB/Swiss-Prot
  ENSRNOT00055013195 UniProtKB/Swiss-Prot
  ENSRNOT00060021869 UniProtKB/Swiss-Prot
  ENSRNOT00065015168 UniProtKB/Swiss-Prot
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096152 IMAGE-MGC_LOAD
InterPro bHLH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TAL-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304663 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93688 IMAGE-MGC_LOAD
NCBI Gene 304663 ENTREZGENE
PANTHER PROTEIN LYL-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13864 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lyl1 PhenoGen
PROSITE BHLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002950 RatGTEx
  ENSRNOG00055007859 RatGTEx
  ENSRNOG00060012865 RatGTEx
  ENSRNOG00065009482 RatGTEx
SMART HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP HLH, helix-loop-helix DNA-binding domain UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6IY78_RAT UniProtKB/TrEMBL
  LYL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-29 Lyl1  LYL1, basic helix-loop-helix family member  Lyl1  lymphoblastic leukemia associated hematopoiesis regulator 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-02-04 Lyl1  lymphoblastic leukemia associated hematopoiesis regulator 1  Lyl1  lymphoblastic leukemia derived sequence 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Lyl1  lymphoblastic leukemia derived sequence 1  LOC100365743  protein lyl-1-like  Data merged from RGD:2318442 1643240 APPROVED
2010-05-05 LOC100365743  protein lyl-1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Lyl1  lymphoblastic leukemia derived sequence 1      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Lyl1  lymphoblastic leukemia derived sequence 1      Symbol and Name status set to provisional 70820 PROVISIONAL