Tbio LMO1 Rhombotin-1

Protein Summary

Description

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors. This locus encodes a transcriptional regulator that contains two cysteine-rich LIM domains but lacks a DNA-binding domain. LIM domains may play a role in protein interactions; thus the encoded protein may regulate transcription by competitively binding to specific DNA-binding transcription factors. Alterations at this locus have been associated with acute lymphoblastic T-cell leukemia. Chromosomal rearrangements have been observed between this locus and at least two loci, the delta subunit of the T-cell antigen receptor gene and the LIM domain binding 1 gene. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2012]

Uniprot Accession IDs

• P25800
• E9PSF5
• Q4VBC5
• Q8IXR0

Gene Name

• LMO1

Ensembl ID

• ENST00000335790
• ENSP00000338207
• ENSG00000166407
• ENST00000428101
• ENSP00000404538

Symbol

• RBTN1
• RHOM1
• TTG1
• TTG1
• RBTN1
• RHOM1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
gene perturbation	0.8
PubMedID	0.72
transcription factor binding site profile	0.71
trait	0.61
transcription factor	0.56

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 63.32   (req: < 5)

Gene RIFs: 17   (req: <= 3)

Antibodies: 145   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 63.32   (req: >= 5)

Gene RIFs: 17   (req: > 3)

Antibodies: 145   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 5

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (5)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
neuroblastoma	EFO_0000621	3	2	0	1.3	78.2
parental genotype effect measurement	EFO_0005939	1	1	1		73.7
birth weight	EFO_0004344	1	1	1		73.7
body height	EFO_0004339	1	1	1		21.5
glucose measurement	EFO_0004468	1	1	1		17.8

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 5

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
neuroblastoma	EFO_0000621	0	1.3	78.2
parental genotype effect measurement	EFO_0005939	1		73.7
birth weight	EFO_0004344	1		73.7
body height	EFO_0004339	1		21.5
glucose measurement	EFO_0004468	1		17.8

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Orthologs (10)

1 – 5 of 10

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	LIM domain only 1	VGNC:3249	749084
Macaque	LIM domain only 1		100425589
Mouse	LIM domain only 1	MGI:102812	109594
Dog	LIM domain only 1	VGNC:42722	610473
Horse	LIM domain only 1	VGNC:19709	100055468

Species	Name	OMA	EggNOG	Inparanoid
Chimp	LIM domain only 1
Macaque	LIM domain only 1
Mouse	LIM domain only 1
Dog	LIM domain only 1
Horse	LIM domain only 1

Protein Structure (0 Structures, 1 AlphaFold Model)

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Representation

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Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

AF-P25800-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

Pathways (5)

Reactome (5)

Gene expression (Transcription) (R-HSA-74160)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Gene expression (Transcription)	1452 targets	R-HSA-74160
Reactome	Generic Transcription Pathway	1195 targets	R-HSA-212436
Reactome	RNA Polymerase II Transcription	1314 targets	R-HSA-73857
Reactome	RUNX1 regulates transcription of genes involved in differentiation of HSCs	100 targets	R-HSA-8939236
Reactome	Transcriptional regulation by RUNX1	208 targets	R-HSA-8878171

Name	Explore in Pharos	Explore in Source
Gene expression (Transcription)	1452 targets	R-HSA-74160
Generic Transcription Pathway	1195 targets	R-HSA-212436
RNA Polymerase II Transcription	1314 targets	R-HSA-73857
RUNX1 regulates transcription of genes involved in differentiation of HSCs	100 targets	R-HSA-8939236
Transcriptional regulation by RUNX1	208 targets	R-HSA-8878171

Gene Ontology Terms (7)

Functions (1)

Components (2)

Processes (4)

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10

1 – 1 of 1

GO Term	Evidence	Assigned by
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Protein-Protein Interactions (103)

Explore Interacting Targets

1 – 10 of 103

• See Interactions on String-DB

LMO3

Tbio

Novelty:  0.03437083

p_int:  0.999999997

p_wrong:  3e-9

Data Source:  BioPlex

ZBTB43

Tdark

Family:  TF

Novelty:  0.35735342

p_int:  0.999999996

p_ni:  3e-9

Data Source:  BioPlex

DNAAF2

Tbio

Novelty:  0.01254416

p_int:  0.999999993

p_ni:  6e-9

Data Source:  BioPlex

LDB1

Tbio

Novelty:  0.01110112

p_int:  0.999999987

p_ni:  1.3e-8

Score:  0.995

Data Source:  BioPlex,STRINGDB

MN1

Tbio

Novelty:  0.0015395

p_int:  0.999999985

p_ni:  1.5e-8

Data Source:  BioPlex

TRIO

Tbio

Family:  Kinase

Novelty:  0.03113573

p_int:  0.999999979

p_ni:  2e-8

p_wrong:  1e-9

Data Source:  BioPlex

UBE3D

Tbio

Family:  Enzyme

Novelty:  0.44919491

p_int:  0.999999972

p_ni:  2.8e-8

Data Source:  BioPlex

SSBP3

Tbio

Novelty:  0.01955714

p_int:  0.999999965

p_ni:  3.5e-8

Score:  0.512

Data Source:  BioPlex,STRINGDB

SSBP4

Tdark

Novelty:  0.27365687

p_int:  0.999999789

p_ni:  1.82e-7

p_wrong:  2.9e-8

Score:  0.262

Data Source:  BioPlex,STRINGDB

SSBP2

Tbio

Novelty:  0.06546999

p_int:  0.999999443

p_ni:  5.54e-7

p_wrong:  4e-9

Score:  0.528

Data Source:  BioPlex,STRINGDB

Publication Statistics

PubMed Score  63.32

PubMed score by year

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PubTator Score  40.39

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

No Header	No Header
Alternative splicing
Chromosomal rearrangement
Complete proteome
LIM domain
Metal-binding
Nucleus
Proto-oncogene
Reference proteome
Repeat
Zinc

GWAS Trait Find Similar Targets

No Header	No Header
birth weight
body height
glucose measurement
neuroblastoma
parental genotype effect measurement