LYL1 (LYL1 basic helix-loop-helix family member) - Rat Genome Database
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Gene: LYL1 (LYL1 basic helix-loop-helix family member) Homo sapiens
Analyze
Symbol: LYL1
Name: LYL1 basic helix-loop-helix family member
RGD ID: 1343769
HGNC Page HGNC
Description: Exhibits DNA binding activity. Involved in blood vessel maturation and positive regulation of transcription, DNA-templated. Predicted to localize to nuclear chromatin. Implicated in T-cell acute lymphoblastic leukemia.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: bHLHa18; class A basic helix-loop-helix protein 18; LYL1, basic helix-loop-helix family member; lymphoblastic leukemia associated hematopoiesis regulator 1; lymphoblastic leukemia derived sequence 1; lymphoblastic leukemia-derived sequence 1; protein lyl-1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1913,099,033 - 13,103,161 (-)EnsemblGRCh38hg38GRCh38
GRCh381913,099,033 - 13,102,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,208,002 - 13,213,974 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,070,847 - 13,074,681 (-)NCBINCBI36hg18NCBI36
Build 341913,070,847 - 13,074,681NCBI
Celera1913,100,251 - 13,104,085 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,782,481 - 12,786,613 (-)NCBIHuRef
CHM1_11913,210,856 - 13,214,988 (-)NCBICHM1_1
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
chromatin  (IBA,ISA)
nucleus  (IEA)

References

Additional References at PubMed
PMID:1763056   PMID:2067848   PMID:2268576   PMID:2752424   PMID:7957052   PMID:8432525   PMID:8628307   PMID:8649774   PMID:9242638   PMID:10023675   PMID:12477932   PMID:15057824  
PMID:15489334   PMID:16094422   PMID:16344560   PMID:18160048   PMID:19176012   PMID:19274049   PMID:19497860   PMID:19608273   PMID:19671288   PMID:20418284   PMID:20603019   PMID:20844761  
PMID:21873635   PMID:23327922   PMID:23812588   PMID:26593974   PMID:26598620   PMID:29716549   PMID:30755707  


Genomics

Comparative Map Data
LYL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1913,099,033 - 13,103,161 (-)EnsemblGRCh38hg38GRCh38
GRCh381913,099,033 - 13,102,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,208,002 - 13,213,974 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,070,847 - 13,074,681 (-)NCBINCBI36hg18NCBI36
Build 341913,070,847 - 13,074,681NCBI
Celera1913,100,251 - 13,104,085 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,782,481 - 12,786,613 (-)NCBIHuRef
CHM1_11913,210,856 - 13,214,988 (-)NCBICHM1_1
Lyl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,428,051 - 85,432,876 (+)NCBIGRCm39mm39
GRCm38884,701,423 - 84,704,716 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,701,449 - 84,704,940 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,225,356 - 87,228,615 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,591,649 - 87,594,797 (+)NCBImm8
Celera889,001,525 - 89,004,783 (+)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.02NCBI
Lyl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,120,059 - 25,122,926 (-)NCBI
Celera1923,005,834 - 23,008,676 (-)NCBICelera
Cytogenetic Map19q11NCBI
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
PanPan1.11913,404,544 - 13,415,231 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,407,596 - 13,409,309 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,660,548 - 12,664,513 (-)NCBIMhudiblu_PPA_v0panPan3
LYL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,109,358 - 49,113,911 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Lyl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 65,955,017 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl611,780,766 - 11,782,618 (-)Ensembl
ChlSab1.1611,778,634 - 11,785,474 (-)NCBI
Lyl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901645,263 - 648,550 (-)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:881
Count of miRNA genes:591
Interacting mature miRNAs:684
Transcripts:ENST00000264824, ENST00000590120, ENST00000590974
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


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 sensory system visual system adipose tissue appendage entire extraembryonic component
High
Medium 528 1229 266 23 1531 15 1153 205 617 26 666 706 8 789 663 1
Low 1830 1757 1413 562 395 409 3123 1918 3017 350 722 787 159 415 2100 2
Below cutoff 67 1 44 36 18 40 71 58 69 30 56 92 5 1 25 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000264824   ⟹   ENSP00000264824
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,099,033 - 13,102,858 (-)Ensembl
RefSeq Acc Id: ENST00000590120
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,101,178 - 13,102,724 (-)Ensembl
RefSeq Acc Id: ENST00000590974   ⟹   ENSP00000468122
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,100,690 - 13,103,161 (-)Ensembl
RefSeq Acc Id: NM_005583   ⟹   NP_005574
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,099,033 - 13,102,858 (-)NCBI
GRCh371913,208,002 - 13,213,974 (-)NCBI
Build 361913,070,847 - 13,074,681 (-)NCBI Archive
HuRef1912,782,481 - 12,786,613 (-)ENTREZGENE
CHM1_11913,210,856 - 13,214,988 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_005574   ⟸   NM_005583
- UniProtKB: P12980 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000468122   ⟸   ENST00000590974
RefSeq Acc Id: ENSP00000264824   ⟸   ENST00000264824
Protein Domains
bHLH

Promoters
RGD ID:6811659
Promoter ID:HG_ACW:40084
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:LYL1.DAPR07-UNSPLICED
Position:
Human AssemblyChrPosition (strand)Source
Build 361913,073,096 - 13,073,596 (-)MPROMDB
RGD ID:6795783
Promoter ID:HG_KWN:29052
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell_12Hour,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_005583
Position:
Human AssemblyChrPosition (strand)Source
Build 361913,074,516 - 13,075,016 (-)MPROMDB
RGD ID:7238769
Promoter ID:EPDNEW_H25131
Type:initiation region
Name:LYL1_2
Description:LYL1, basic helix-loop-helix family member
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H25132  EPDNEW_H25133  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,102,715 - 13,102,775EPDNEW
RGD ID:7238771
Promoter ID:EPDNEW_H25132
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/)
Alternative Promoters:null; see alsoEPDNEW_H25131  EPDNEW_H25133  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,102,854 - 13,102,914EPDNEW
RGD ID:7238775
Promoter ID:EPDNEW_H25133
Type:initiation region
Name:LYL1_3
Description:LYL1, basic helix-loop-helix family member
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H25131  EPDNEW_H25132  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,103,176 - 13,103,236EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000019.9:g.(?_13106632)_(13428155_?)del deletion Marshall-Smith syndrome [RCV000543828] Chr19:13106632..13428155 [GRCh37]
Chr19:19p13.2
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13
likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:10315258-14048994)x3 copy number gain See cases [RCV000052909] Chr19:10315258..14048994 [GRCh38]
Chr19:10425934..14159806 [GRCh37]
Chr19:10286934..14020806 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12132052-14751798)x3 copy number gain See cases [RCV000052910] Chr19:12132052..14751798 [GRCh38]
Chr19:12242867..14862610 [GRCh37]
Chr19:12103867..14723610 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.13(chr19:12850595-13290954)x3 copy number gain See cases [RCV000052911] Chr19:12850595..13290954 [GRCh38]
Chr19:12961409..13401768 [GRCh37]
Chr19:12822409..13262768 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.13(chr19:12813597-13119698)x3 copy number gain See cases [RCV000054144] Chr19:12813597..13119698 [GRCh38]
Chr19:12924411..13230512 [GRCh37]
Chr19:12785411..13091512 [NCBI36]
Chr19:19p13.13
uncertain significance
GRCh38/hg38 19p13.2-13.12(chr19:11227942-14532135)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053944]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053944]|See cases [RCV000053944] Chr19:11227942..14532135 [GRCh38]
Chr19:11338618..14642947 [GRCh37]
Chr19:11199618..14503947 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:11517825-13225287)x1 copy number loss See cases [RCV000053945] Chr19:11517825..13225287 [GRCh38]
Chr19:11628640..13336101 [GRCh37]
Chr19:11489640..13197101 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31
pathogenic
GRCh38/hg38 19p13.13(chr19:13034666-13283686)x1 copy number loss See cases [RCV000135352] Chr19:13034666..13283686 [GRCh38]
Chr19:13145480..13394500 [GRCh37]
Chr19:13006480..13255500 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.13(chr19:12978943-13236134)x3 copy number gain See cases [RCV000136559] Chr19:12978943..13236134 [GRCh38]
Chr19:13089757..13346948 [GRCh37]
Chr19:12950757..13207948 [NCBI36]
Chr19:19p13.13
likely pathogenic|uncertain significance
GRCh38/hg38 19p13.2-13.12(chr19:12580427-14742673)x1 copy number loss See cases [RCV000135937] Chr19:12580427..14742673 [GRCh38]
Chr19:12691241..14853485 [GRCh37]
Chr19:12552241..14714485 [NCBI36]
Chr19:19p13.2-13.12
pathogenic|likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:11525163-14155021)x1 copy number loss See cases [RCV000136909] Chr19:11525163..14155021 [GRCh38]
Chr19:11635978..14265833 [GRCh37]
Chr19:11496978..14126833 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.13(chr19:12974394-13408586)x1 copy number loss See cases [RCV000138197] Chr19:12974394..13408586 [GRCh38]
Chr19:13085208..13519400 [GRCh37]
Chr19:12946208..13380400 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:10319474-13777860)x1 copy number loss See cases [RCV000141568] Chr19:10319474..13777860 [GRCh38]
Chr19:10430150..13888674 [GRCh37]
Chr19:10291150..13749674 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
GRCh37/hg19 19p13.2(chr19:13180583-13319148)x3 copy number gain See cases [RCV000449427] Chr19:13180583..13319148 [GRCh37]
Chr19:19p13.2
likely pathogenic
GRCh37/hg19 19p13.2(chr19:12204632-13497073)x1 copy number loss See cases [RCV000449161] Chr19:12204632..13497073 [GRCh37]
Chr19:19p13.2
pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:9678768-14853426) copy number gain See cases [RCV000446985] Chr19:9678768..14853426 [GRCh37]
Chr19:19p13.2-13.12
pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:12574343-14726197)x1 copy number loss See cases [RCV000511130] Chr19:12574343..14726197 [GRCh37]
Chr19:19p13.2-13.12
pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:11608072-14543046)x3 copy number gain See cases [RCV000511013] Chr19:11608072..14543046 [GRCh37]
Chr19:19p13.2-13.12
uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.2(chr19:12354642-13424014)x1 copy number loss not provided [RCV000846538] Chr19:12354642..13424014 [GRCh37]
Chr19:19p13.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6734 AgrOrtholog
COSMIC LYL1 COSMIC
Ensembl Genes ENSG00000104903 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000264824 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000468122 UniProtKB/TrEMBL
Ensembl Transcript ENST00000264824 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000590974 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot
GTEx ENSG00000104903 GTEx
HGNC ID HGNC:6734 ENTREZGENE
Human Proteome Map LYL1 Human Proteome Map
InterPro bHLH_dom UniProtKB/Swiss-Prot
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot
  TAL-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:4066 UniProtKB/Swiss-Prot
NCBI Gene 4066 ENTREZGENE
OMIM 151440 OMIM
PANTHER PTHR13864 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HLH UniProtKB/Swiss-Prot
PharmGKB PA30497 PharmGKB
PROSITE BHLH UniProtKB/Swiss-Prot
SMART HLH UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot
UniGene Hs.46446 ENTREZGENE
  Hs.728534 ENTREZGENE
UniProt K7ER61_HUMAN UniProtKB/TrEMBL
  LYL1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O76102 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 LYL1  LYL1 basic helix-loop-helix family member    LYL1, basic helix-loop-helix family member  Symbol and/or name change 5135510 APPROVED
2016-06-28 LYL1  LYL1, basic helix-loop-helix family member    lymphoblastic leukemia associated hematopoiesis regulator 1  Symbol and/or name change 5135510 APPROVED
2014-01-29 LYL1  lymphoblastic leukemia associated hematopoiesis regulator 1    lymphoblastic leukemia derived sequence 1  Symbol and/or name change 5135510 APPROVED