LOC100524517 (left-right determination factor 2)

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Gene: LOC100524517 (left-right determination factor 2) Sus scrofa

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Symbol:

LOC100524517

Name:

left-right determination factor 2

RGD ID:

13941754

Description:

ENCODES a protein that exhibits nodal binding (ortholog); INVOLVED IN anterior/posterior axis specification (ortholog); cell migration involved in gastrulation (ortholog); cell population proliferation (ortholog); ASSOCIATED WITH gastrointestinal stromal tumor (ortholog); myocardial infarction (ortholog); parathyroid carcinoma (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred)

Type:

protein-coding

RefSeq Status:

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	10	13,815,157 - 13,819,249 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	10	15,951,740 - 15,974,455 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

gastrointestinal stromal tumor (ISO)

myocardial infarction (ISO)

parathyroid carcinoma (ISO)

Tubulointerstitial Fibrosis (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior axis specification (IBA,ISO)

cell migration involved in gastrulation (ISO)

cell population proliferation (ISO)

determination of left/right symmetry (ISO)

heart morphogenesis (ISO)

negative regulation of cell population proliferation (ISO)

negative regulation of nodal receptor complex assembly (ISO)

negative regulation of nodal signaling pathway (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

response to retinoic acid (ISO)

signal transduction (IEA)

Cellular Component

extracellular region (IEA)

extracellular space (IBA,IEA)

Molecular Function

cytokine activity (IBA,IEA)

growth factor activity (IEA)

nodal binding (ISO)

transforming growth factor beta receptor binding (IEA)

References

Additional References at PubMed

PMID:14681463	PMID:17145712	PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

LOC100524517
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	10	13,815,157 - 13,819,249 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	10	15,951,740 - 15,974,455 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LEFTY1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	225,886,282 - 225,889,146 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	225,886,282 - 225,911,382 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	226,073,982 - 226,076,846 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	224,140,605 - 224,143,459 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	222,380,717 - 222,383,571	NCBI
Celera	1	199,265,024 - 199,267,877 (-)	NCBI		Celera
Cytogenetic Map	1	q42.12	NCBI
HuRef	1	196,591,667 - 196,594,530 (-)	NCBI		HuRef
CHM1_1	1	227,346,296 - 227,349,159 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	225,074,031 - 225,076,895 (-)	NCBI		T2T-CHM13v2.0

Lefty1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	180,762,587 - 180,765,966 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	180,762,587 - 180,765,965 (+)	Ensembl		GRCm39 Ensembl
GRCm38	1	180,935,022 - 180,938,401 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	180,935,022 - 180,938,400 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	182,865,170 - 182,868,532 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	1	182,771,734 - 182,775,075 (+)	NCBI		MGSCv36	mm8
Celera	1	187,999,497 - 188,003,975 (+)	NCBI		Celera
Cytogenetic Map	1	H4	NCBI
cM Map	1	84.46	NCBI

Lefty1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	95,188,091 - 95,191,488 (+)	NCBI		GRCr8
mRatBN7.2	13	92,649,226 - 92,659,722 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	92,656,323 - 92,659,720 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	13	95,161,640 - 95,165,037 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	96,561,569 - 96,564,966 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	93,736,266 - 93,739,663 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	99,212,778 - 99,217,786 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	99,214,389 - 99,217,786 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	13	104,212,236 - 104,215,633 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	96,664,408 - 96,667,805 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	13	92,199,283 - 92,202,680 (+)	NCBI		Celera
Cytogenetic Map	13	q26	NCBI

LOC100969502
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	23,638,440 - 23,651,563 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	23,586,789 - 23,599,910 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	201,347,411 - 201,351,295 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	206,347,974 - 206,351,201 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	206,348,419 - 206,350,787 (-)	Ensembl	panpan1.1		panPan2

LEFTY1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	38,932,668 - 38,934,989 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	38,414,884 - 38,417,205 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	38,766,526 - 38,768,964 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	7	38,606,312 - 38,608,748 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	38,614,462 - 38,616,899 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	38,884,233 - 38,886,670 (+)	NCBI		UU_Cfam_GSD_1.0

LOC103230001
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	25	3,881,085 - 3,884,596 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	3,881,837 - 3,884,151 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666055	3,886,974 - 3,891,002 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in LOC100524517
159 total Variants

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

ectoderm	nervous system
11	11

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003130541	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000071	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK389998	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK393243	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01063632	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_003130541 ⟹ XP_003130589

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	10	13,815,157 - 13,819,249 (-)	NCBI

Sequence:

show sequence

TCAATTTCAGCTGTACAGCAAAGTGACCCAGCCATACATATATATACATTCTTTTTCTCATATT
ATCTTCCATCATGTTCTATGACAAGTGACTGGATATCGTTGCCTTTGCTGTACAGCATGGAAAC
AGCTTTTTAACTGAGCAGGCACCCAAAGCCAAGGCAGAGGCTTGTGACCACAAAAATAGCCATC
TGTCCACAGTCCAGACAGGCCTTTGTGCCCTTCTAGACAGCCCCCTCCTCGGGCTCAGGGAAAC
TGTCTGGCTGCTGAGCTCCCAGGAGGTCTGAGGGGTGTGACCTCCCTCCCTCCTTCCCTCCCTC
CCTCCACCCAGGCCCAGCCCAGGGCCGCCTATAAAGCTGGCCCAGCCTGGCTCTCAGCACTCCA
GCTGGGACCCTCCTGAGCCTCCTCCGGGGGCCACGTCCACTCTGCCCCTCCTTCTCGCCAGCAG
CACCATGCGGGCCCTGTGGCTCTGCTGGGCACTCTGGGCACTGCCCCTGGCCGGCCCCGGGGCG
GCCCTGACCGAGCAGCAGATCCTGGGCAGCCTGCTGCAGCAGCTGCACCTCAGCGAGGTGCCCG
CCCTGGACAAGGCCGACGTGGACGGGCTGGTCATCCCTGCCCAGGTGCGGGCCCAGTACGTGGC
CCTGCTGCAGCGCAGCCACGGGGCCCGCTCCCGGGGGAAGAGGTTCAGCCAGAACTTCCGAGAG
GTGGTTGGCAGGTTCCTGCTGTCCGAGGCCTCCACGCACCTGCTGGTGTTCGACATGGAGCAGC
GGCTGCCGCCCCACAGCGAGCTGGTGCAGGCGGTGCTGCGCCTCTTCCAGGAGCCGGTCCCCAA
GGCCGCGCTCCGCCGGCACGAGCGGCTCTTCCCGCGCAGCGACCGCGCCCGGGTCACCGTCCAG
TGGCTGCACATCCGCGAGGACGGCTCCAACCGCACCTCCCTCATCGACTCCAGGCTGGTGTCCA
TCCACGAGAGCGGCTGGCAGGCCCTGGACGTGACGGAGGCGGTGACCTTCTGGCAGCAGCTGCG
CCGGCCCCGGCAGCCGCTGCTGCTGCAGGTGTCTGTGCAGCGGGAGCCCCCGGGCCCGCGGGGC
TCGGACGCCCACAGGCTGGTCCGCTTCGCCTCCCAGGGGCCGTCGGGCGGCGGGCAGGGGGAGC
CGCAGCTGGAGCTGCACACCCTGGACCTCAGGGACTACGGAGCTCAGGGAAATTGTGACCCGAA
GGCGCCAGTGACCGAGGGCACCCGCTGCTGCCGCCAGGAGATGTACATTGACCTGCAGGGGATG
AAATGGGCTGAGAACTGGGTCCTGGAGCCCCCGGGCTTCCTGGCCTATGAGTGTGTGGGCACCT
GCCAGCAGCCCCCCGAGCCCCTGGCCTTCAGGTGGCCATTTCTGGGGCCTCGCCAGTGCATCGC
CTCGGAGACAACCTCGTTGCCCGTGATCGTCAGCATCCAGGAGGGCGGCAAGCCCAGGCCCCAG
GTGGTCAGCCTGCCCAACATGAGGGTGNAAGAGTGCAGCTGTGCCTGGGATGGGGCGCCCGTGC
CAAGGAAGCTGGAGCCGTAGGCACAGCATGCAGCCATAGAGAGACTTGGCTTCCGTGTGTGTCA
GCAATGTTCTAGGGCACCAGGAGAGATGGGGGTTATTGAGCTGCCAATGACACATACTCTGGGC
TTTCTACTGGACTCTTCTGACCAGTCAGTTCACCCCCTAATTTGTTTCCCAGGAACAAGACTCT
CTGGCCACTGGTTAGCCCCCACCCAGTCTTCGTTCTTCTTGACTGCACTGTATTATTCAGCGCA
CTGTATCCTAAGCACTTACCTGTGTAGATTTTGTAACCTAAGAGCAGAAACCCCAGTCTGTCAT
TGTTACCCTGTCCTGTCACTGGCTCTGGGCTGAGCTTGGTGCTATGGGTGGGAGATGGGGCTGC
TACTCTGGGCTTAAAACCTAGGGTCAAGTATGGGCTGTGCAATCCCAACTCAGATACTAAGAGA
ATTCTGCAAGAGGTAAAGAAAACCCATTTTATTCTGTATTTCTGTTTTACCCAGTACCCTGCAA
ATTGTGAGGAAACAGAAAATTCTATCAGGATTAGGTCAATCAGATAAGAAAACTTAAGGAAAGA
GCTAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_003130589	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000011575
	ENSSSCP00000011575.3
	ENSSSCP00045047468.1
	ENSSSCP00065017525.1

RefSeq Acc Id:

XP_003130589 ⟸ XM_003130541

- UniProtKB:

A0A8D2C4T2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MRALWLCWALWALPLAGPGAALTEQQILGSLLQQLHLSEVPALDKADVDGLVIPAQVRAQYVAL
LQRSHGARSRGKRFSQNFREVVGRFLLSEASTHLLVFDMEQRLPPHSELVQAVLRLFQEPVPKA
ALRRHERLFPRSDRARVTVQWLHIREDGSNRTSLIDSRLVSIHESGWQALDVTEAVTFWQQLRR
PRQPLLLQVSVQREPPGPRGSDAHRLVRFASQGPSGGGQGEPQLELHTLDLRDYGAQGNCDPKA
PVTEGTRCCRQEMYIDLQGMKWAENWVLEPPGFLAYECVGTCQQPPEPLAFRWPFLGPRQCIAS
ETTSLPVIVSIQEGGKPRPQVVSLPNMRVXECSCAWDGAPVPRKLEP

hide sequence

Protein Domains

TGF-beta family profile

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000038188	ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00045038528	UniProtKB/TrEMBL
	ENSSSCG00065030564	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000011879	ENTREZGENE
	ENSSSCT00000011879.3	UniProtKB/TrEMBL
	ENSSSCT00045066869.1	UniProtKB/TrEMBL
	ENSSSCT00065041316.1	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	ssc:100524517	UniProtKB/TrEMBL
NCBI Gene	LOC100524517	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	A0A8D1JBG9_PIG	UniProtKB/TrEMBL
	A0A8D2C4T2	ENTREZGENE, UniProtKB/TrEMBL
	F1S8R0_PIG	UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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