LOC490387 (left-right determination factor 1) - Rat Genome Database

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Gene: LOC490387 (left-right determination factor 1) Canis lupus familiaris
Analyze
Symbol: LOC490387
Name: left-right determination factor 1
RGD ID: 12184422
Description: ENCODES a protein that exhibits cytokine activity (inferred); growth factor activity (inferred); transforming growth factor beta receptor binding (inferred); INVOLVED IN anterior/posterior axis specification (inferred); signal transduction (inferred); ASSOCIATED WITH congenital heart disease (ortholog); Experimental Liver Cirrhosis (ortholog); Female Infertility (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: left-right determination factor 2; LEFTY2
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1738,893,456 - 38,898,741 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha738,374,116 - 38,379,043 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0738,725,973 - 38,730,861 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1738,565,731 - 38,570,636 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0738,573,876 - 38,578,786 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0738,843,706 - 38,848,590 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LOC490387
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1738,893,456 - 38,898,741 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha738,374,116 - 38,379,043 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0738,725,973 - 38,730,861 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1738,565,731 - 38,570,636 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0738,573,876 - 38,578,786 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0738,843,706 - 38,848,590 (+)NCBIUU_Cfam_GSD_1.0
LEFTY2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381225,936,603 - 225,941,220 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1225,936,598 - 225,941,383 (-)EnsemblGRCh38hg38GRCh38
GRCh371226,124,303 - 226,128,920 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361224,190,926 - 224,195,543 (-)NCBINCBI36Build 36hg18NCBI36
Build 341222,431,037 - 222,435,655NCBI
Celera1199,315,346 - 199,320,132 (-)NCBICelera
Cytogenetic Map1q42.12NCBI
HuRef1196,642,011 - 196,646,798 (-)NCBIHuRef
CHM1_11227,396,616 - 227,401,402 (-)NCBICHM1_1
T2T-CHM13v2.01225,124,381 - 225,129,000 (-)NCBIT2T-CHM13v2.0
Lefty2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391180,720,673 - 180,726,672 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1180,720,673 - 180,726,668 (+)EnsemblGRCm39 Ensembl
GRCm381180,893,108 - 180,899,107 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1180,893,108 - 180,899,103 (+)EnsemblGRCm38mm10GRCm38
MGSCv371182,823,250 - 182,829,234 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361182,729,794 - 182,735,778 (+)NCBIMGSCv36mm8
Celera1187,956,284 - 187,961,909 (+)NCBICelera
Cytogenetic Map1H4NCBI
cM Map184.46NCBI
LEFTY2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2123,595,526 - 23,600,725 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1123,544,101 - 23,549,080 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01201,398,235 - 201,402,906 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11206,397,118 - 206,401,948 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1206,397,118 - 206,401,839 (-)Ensemblpanpan1.1panPan2
LOC100524517
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11013,815,157 - 13,819,249 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21015,951,740 - 15,974,455 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103229999
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1253,828,944 - 3,834,679 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl253,830,059 - 3,833,847 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660553,836,858 - 3,841,603 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lefty2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480771,011 - 75,210 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LOC490387
48 total Variants

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 hemolymphoid system integumental system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 3 2 1
Below cutoff 4 13 3 4 9 8 9 5

Sequence


Reference Sequences
RefSeq Acc Id: XM_038481472   ⟹   XP_038337400
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1738,565,731 - 38,570,636 (+)NCBI
RefSeq Acc Id: XM_038542825   ⟹   XP_038398753
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0738,843,706 - 38,848,590 (+)NCBI
RefSeq Acc Id: XM_038606967   ⟹   XP_038462895
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0738,573,876 - 38,578,786 (+)NCBI
RefSeq Acc Id: XM_038671668   ⟹   XP_038527596
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0738,725,973 - 38,730,861 (+)NCBI
RefSeq Acc Id: XM_547508   ⟹   XP_547508
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1738,893,456 - 38,898,741 (+)NCBI
Dog10K_Boxer_Tasha738,374,116 - 38,379,043 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_547508   ⟸   XM_547508
- UniProtKB: A0A8C0SBM0 (UniProtKB/TrEMBL),   A0A8C0JRZ4 (UniProtKB/TrEMBL),   A0A8P0NHK2 (UniProtKB/TrEMBL),   A0A8I3RUX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038337400   ⟸   XM_038481472
RefSeq Acc Id: XP_038462895   ⟸   XM_038606967
RefSeq Acc Id: XP_038527596   ⟸   XM_038671668
- UniProtKB: A0A8I3RUX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038398753   ⟸   XM_038542825
- UniProtKB: A0A8I3RUX2 (UniProtKB/TrEMBL)
Protein Domains
TGF-beta family profile


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000016127 UniProtKB/TrEMBL
  ENSCAFG00030004725 UniProtKB/TrEMBL
  ENSCAFG00040011902 UniProtKB/TrEMBL
  ENSCAFG00845008972 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000025590.4 UniProtKB/TrEMBL
  ENSCAFT00000071907.2 UniProtKB/TrEMBL
  ENSCAFT00030008687.1 UniProtKB/TrEMBL
  ENSCAFT00040021917.1 UniProtKB/TrEMBL
  ENSCAFT00845015797 ENTREZGENE
  ENSCAFT00845015797.1 UniProtKB/TrEMBL
  ENSCAFT00845015822.1 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/TrEMBL
  2.60.120.970 UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/TrEMBL
  LRDF UniProtKB/TrEMBL
  TGF-b_C UniProtKB/TrEMBL
  TGF-b_propeptide UniProtKB/TrEMBL
  TGF-beta-rel UniProtKB/TrEMBL
  TGFb_CS UniProtKB/TrEMBL
KEGG Report cfa:490387 UniProtKB/TrEMBL
NCBI Gene LEFTY2 ENTREZGENE
PANTHER LEFT-RIGHT DETERMINATION FACTOR UniProtKB/TrEMBL
  PTHR11848 UniProtKB/TrEMBL
Pfam TGF_beta UniProtKB/TrEMBL
  TGFb_propeptide UniProtKB/TrEMBL
PIRSF TGFb4 UniProtKB/TrEMBL
PRINTS TGFBETA4 UniProtKB/TrEMBL
PROSITE TGF_BETA_1 UniProtKB/TrEMBL
  TGF_BETA_2 UniProtKB/TrEMBL
SMART TGFB UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/TrEMBL
UniProt A0A8C0JRZ4 ENTREZGENE
  A0A8C0SBM0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3RUX2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3RWG6_CANLF UniProtKB/TrEMBL
  A0A8P0NHK2 ENTREZGENE
  A0A8P0P5I4_CANLF UniProtKB/TrEMBL
UniProt Secondary A0A8P0NHK2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-12 LOC490387  left-right determination factor 1  LEFTY2  left-right determination factor 2  Symbol and/or name change 5135510 APPROVED