ELF1

Summary

ELF1 (E74 like ETS transcription factor 1, HGNC:3316) is a protein-coding gene on chromosome 13q14.11, encoding ETS-related transcription factor Elf-1 (P32519). Transcription factor that activates the LYN and BLK promoters.

This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 1997 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 97 total
• GTEx eGene: eQTL in 11 tissues, sQTL in 4 (q < 0.05)
• Constraint (gnomAD): pLI 0.02 (LoF-tolerant), LOEUF 0.66 (unconstrained)
• MANE Select transcript: NM_172373
• Notable: 97 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3316
Approved symbol	ELF1
Name	E74 like ETS transcription factor 1
Location	13q14.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000120690
Ensembl biotype	protein_coding
OMIM	189973
Entrez	1997

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 26 protein_coding, 1 nonsense_mediated_decay

MANE Select: ENST00000239882

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 5: 1

ENST00000239882, ENST00000405737, ENST00000498824, ENST00000625359, ENST00000635415, ENST00000891312, ENST00000891313, ENST00000891314, ENST00000891315, ENST00000891316, ENST00000891317, ENST00000891318, ENST00000891319, ENST00000891320, ENST00000891321, ENST00000891322, ENST00000891323, ENST00000891324, ENST00000891325, ENST00000891326, ENST00000955689, ENST00000955690, ENST00001108542, ENST00001108543, ENST00001108544, ENST00001126235, ENST00001132181

RefSeq mRNA: 6 — MANE Select: NM_172373 NM_001145353, NM_001370329, NM_001370330, NM_001370331, NM_001370332, NM_172373

CCDS: CCDS45043, CCDS9374

Canonical transcript exons

ENST00000239882 — 9 exons

Exon	Start	End
ENSE00001481322	40931924	40934028
ENSE00001481348	41019228	41019316
ENSE00003481363	40958836	40959016
ENSE00003606490	40940921	40941370
ENSE00003613988	40949806	40949973
ENSE00003638368	40943842	40943925
ENSE00003675334	40951329	40951436
ENSE00003749140	40942952	40943144
ENSE00003785110	40981983	40982282

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 99.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.3154 / max 1717.2129, expressed in 1809 samples.

Highest expression (Bgee): secondary oocyte, monocyte, mononuclear cell, leukocyte, lymph node.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ELF1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 11 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

15 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells EBV-transformed lymphocytes	sqtl	4.2e-06	+0.56	13:41014326:T:C
Lung	sqtl	4.4e-03	+1.05	13:41278902:G:C
Skin Sun Exposed Lower leg	eqtl	4.9e-03	+0.22	13:40516904:G:A
Heart Left Ventricle	sqtl	7.4e-03	-0.33	13:41033703:A:G
Whole Blood	eqtl	8.0e-03	-0.27	13:41689964:G:A
Thyroid	eqtl	1.3e-02	-0.14	13:40904827:G:A
Stomach	eqtl	1.3e-02	-0.30	13:41962604:T:C
Heart Atrial Appendage	eqtl	1.3e-02	-0.35	13:41053687:G:T
Whole Blood	sqtl	1.7e-02	-0.82	13:41556620:G:T
Nerve Tibial	eqtl	2.0e-02	-0.20	13:41590063:G:GC
Bladder	eqtl	2.7e-02	+2.18	13:40139581:AT:A
Cells Cultured fibroblasts	eqtl	3.1e-02	-0.31	13:40133165:G:C
Ovary	eqtl	3.6e-02	-0.54	13:41436447:C:G
Spleen	eqtl	3.6e-02	-0.18	13:40426764:T:C
Brain Cerebellum	eqtl	4.5e-02	-0.31	13:41707171:T:C

FANTOM5 promoters

showing 10 of 18 alternative TSS:

Promoter ID	TPM avg	Samples expressed
136941	20.1067	1181
136931	10.5779	574
136952	6.3075	1699
136949	3.1692	1323
136946	2.2741	917
136947	1.1886	643
136948	0.8850	524
136939	0.5549	183
136942	0.5378	255
136951	0.5191	254

Top tissues by expression

showing 100 of 293 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.23	gold quality
monocyte	CL:0000576	96.83	gold quality
mononuclear cell	CL:0000842	96.81	gold quality
leukocyte	CL:0000738	96.72	gold quality
lymph node	UBERON:0000029	96.61	gold quality
bone marrow cell	CL:0002092	96.51	gold quality
calcaneal tendon	UBERON:0003701	96.37	gold quality
bone marrow	UBERON:0002371	96.09	gold quality
nipple	UBERON:0002030	96.08	gold quality
vermiform appendix	UBERON:0001154	95.97	gold quality
gall bladder	UBERON:0002110	95.94	gold quality
caecum	UBERON:0001153	95.52	gold quality
pharyngeal mucosa	UBERON:0000355	95.34	gold quality
urethra	UBERON:0000057	95.30	gold quality
rectum	UBERON:0001052	95.21	gold quality
pericardium	UBERON:0002407	95.16	gold quality
penis	UBERON:0000989	94.81	gold quality
blood	UBERON:0000178	94.76	gold quality
islet of Langerhans	UBERON:0000006	94.66	gold quality
thymus	UBERON:0002370	94.61	gold quality
synovial joint	UBERON:0002217	94.59	gold quality
parietal pleura	UBERON:0002400	94.47	gold quality
duodenum	UBERON:0002114	94.46	gold quality
tonsil	UBERON:0002372	94.31	gold quality
pylorus	UBERON:0001166	94.16	gold quality
right lung	UBERON:0002167	94.09	gold quality
mammary duct	UBERON:0001765	94.07	gold quality
colonic epithelium	UBERON:0000397	93.99	gold quality
superficial temporal artery	UBERON:0001614	93.99	gold quality
jejunal mucosa	UBERON:0000399	93.96	gold quality
visceral pleura	UBERON:0002401	93.60	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.55	gold quality
epithelium of mammary gland	UBERON:0003244	93.42	gold quality
oocyte	CL:0000023	93.40	gold quality
palpebral conjunctiva	UBERON:0001812	93.35	gold quality
superior surface of tongue	UBERON:0007371	93.30	gold quality
cervix squamous epithelium	UBERON:0006922	93.27	silver quality
colonic mucosa	UBERON:0000317	93.16	gold quality
tendon	UBERON:0000043	93.10	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.04	gold quality
endometrium	UBERON:0001295	92.93	gold quality
oral cavity	UBERON:0000167	92.70	gold quality
pleura	UBERON:0000977	92.67	gold quality
smooth muscle tissue	UBERON:0001135	92.37	gold quality
peritoneum	UBERON:0002358	92.36	gold quality
omental fat pad	UBERON:0010414	92.36	gold quality
skin of abdomen	UBERON:0001416	92.28	gold quality
esophagus mucosa	UBERON:0002469	92.28	gold quality
pancreas	UBERON:0001264	92.27	gold quality
subcutaneous adipose tissue	UBERON:0002190	92.20	gold quality
granulocyte	CL:0000094	92.17	gold quality
mammary gland	UBERON:0001911	92.13	gold quality
epithelium of nasopharynx	UBERON:0001951	92.11	gold quality
adipose tissue of abdominal region	UBERON:0007808	92.11	gold quality
nasopharynx	UBERON:0001728	92.10	gold quality
thoracic mammary gland	UBERON:0005200	92.10	gold quality
esophagus squamous epithelium	UBERON:0006920	92.06	gold quality
lower lobe of lung	UBERON:0008949	92.06	gold quality
zone of skin	UBERON:0000014	92.00	gold quality
urinary bladder	UBERON:0001255	91.98	gold quality
amniotic fluid	UBERON:0000173	91.97	gold quality
skin of hip	UBERON:0001554	91.92	gold quality
skin of leg	UBERON:0001511	91.90	gold quality
cardia of stomach	UBERON:0001162	91.89	gold quality
minor salivary gland	UBERON:0001830	91.86	gold quality
small intestine	UBERON:0002108	91.79	gold quality
decidua	UBERON:0002450	91.78	gold quality
corpus epididymis	UBERON:0004359	91.78	gold quality
vagina	UBERON:0000996	91.74	gold quality
upper lobe of left lung	UBERON:0008952	91.67	gold quality
descending thoracic aorta	UBERON:0002345	91.66	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.66	gold quality
popliteal artery	UBERON:0002250	91.64	gold quality
tibial artery	UBERON:0007610	91.64	gold quality
upper lobe of lung	UBERON:0008948	91.62	gold quality
nasal cavity mucosa	UBERON:0001826	91.54	gold quality
trabecular bone tissue	UBERON:0002483	91.53	gold quality
spleen	UBERON:0002106	91.50	gold quality
tongue	UBERON:0001723	91.48	gold quality
artery	UBERON:0001637	91.45	gold quality
mouth mucosa	UBERON:0003729	91.45	gold quality
upper leg skin	UBERON:0004262	91.38	gold quality
uterus	UBERON:0000995	91.35	gold quality
connective tissue	UBERON:0002384	91.33	gold quality
adipose tissue	UBERON:0001013	91.32	gold quality
vena cava	UBERON:0004087	91.32	gold quality
ectocervix	UBERON:0012249	91.31	gold quality
uterine cervix	UBERON:0000002	91.24	gold quality
lung	UBERON:0002048	91.22	gold quality
intestine	UBERON:0000160	91.16	gold quality
aorta	UBERON:0000947	91.16	gold quality
bronchial epithelial cell	CL:0002328	91.15	gold quality
body of pancreas	UBERON:0001150	91.13	gold quality
epithelium of esophagus	UBERON:0001976	90.96	gold quality
colon	UBERON:0001155	90.95	gold quality
large intestine	UBERON:0000059	90.92	gold quality
squamous epithelium	UBERON:0006914	90.91	gold quality
left uterine tube	UBERON:0001303	90.87	gold quality
esophagus	UBERON:0001043	90.86	gold quality
transverse colon	UBERON:0001157	90.74	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	27.04
E-HCAD-10	yes	17.96
E-MTAB-9388	yes	14.12
E-CURD-112	yes	10.97
E-MTAB-6701	yes	10.37
E-MTAB-10042	yes	8.47
E-GEOD-130148	yes	6.94
E-GEOD-106540	no	865.13
E-MTAB-6075	no	532.42
E-HCAD-4	no	31.07
E-CURD-46	no	24.07
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 160 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Bone marrow	tissue	189.8	medium
Thymus	tissue	125.3
Frontal cortex	tissue	99.3
Tonsil	tissue	90.8	high
Lymph node	tissue	89.0	high
Caudate putamen	tissue	85.2
Choroid plexus	tissue	84.8
Testis	tissue	81.2	medium
Hippocampus	tissue	75.0	medium
Postcentral gyrus	tissue	72.6
Pituitary gland	tissue	71.0
Nucleus accumbens	tissue	69.5
Spleen	tissue	64.4	medium
Appendix	tissue	60.7	medium
Adipose tissue	tissue	60.1	low
Urinary bladder	tissue	57.3	high
Locus coeruleus	tissue	56.9
Bone marrow	tissue	56.6	low
Gallbladder	tissue	55.8	medium
Small intestine	tissue	54.5	medium
Salivary gland	tissue	53.4	low
Pancreas	tissue	52.9	low
Thyroid gland	tissue	51.4	medium
Duodenum	tissue	50.2	medium
Esophagus	tissue	49.4	medium
Ovary	tissue	49.1	low
Pancreas	tissue	47.6	medium
Liver	tissue	47.2	low
Stomach 1	tissue	46.9	medium
Cerebral cortex	tissue	45.7	high
Vagina	tissue	45.7	medium
Somatosensory cortex	tissue	45.7
Placenta	tissue	45.6	medium
Parathyroid gland	tissue	45.5	medium
Rectum	tissue	45.4	medium
Lung	tissue	44.6	medium
Tongue	tissue	44.2
Pons	tissue	44.1
Thalamus	tissue	44.0
Occipital cortex	tissue	44.0
Thymus	tissue	43.8
Cervix	tissue	43.0	medium
Colon	tissue	42.7	medium
Breast	tissue	42.4	medium
Fallopian tube	tissue	42.3	high
Skeletal muscle	tissue	42.2	not detected
Hippocampal formation	tissue	42.2
Motor cortex	tissue	42.1
Lymph node	tissue	42.0	high
Seminal vesicle	tissue	41.9	medium
Hypothalamus	tissue	41.9
Prefrontal cortex	tissue	41.7
Superior colliculi	tissue	41.7
Smooth muscle	tissue	41.0	not detected
Epididymis	tissue	39.9	medium
Periaqueductal gray	tissue	39.5
Entorhinal cortex	tissue	39.4
Midbrain	tissue	39.2
Septum	tissue	39.0
Fallopian tube	tissue	38.7	medium

Brain sub-regions (HPA Brain Atlas): detected in 383; highest nTPM — Somatomor cortex, precentral gyrus (white matter) (113.7), Area parastriata, superior (102.0), Angular gyrus (white matter) (95.7), Cerebellar cortex (95.1), Preoptic area (93.0).

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA0473.1	ELF1	Ets-related
MA0473.2	ELF1	Ets-related
MA0473.3	ELF1	Ets-related
MA0473.4	ELF1	Ets-related
MA1952.1	FOXJ2::ELF1	FOX,Ets-related
MA1952.2	FOXJ2::ELF1	FOX,Ets-related
MA1953.1	FOXO1::ELF1	FOX,Ets-related
MA1953.2	FOXO1::ELF1	FOX,Ets-related
UN0535.1	FOXO1::ELF1	FOX,Ets-related
UN0535.2	FOXO1::ELF1	FOX,Ets-related
UN0582.1	TEAD4::ELF1	TEF-1-related factors,Ets-related
UN0582.2	TEAD4::ELF1	TEF-1-related factors,Ets-related
UN0929.1	DLX1::ELF1	NK,Ets-related
UN0954.1	ELF1::HOXC10	Ets-related,HOX
UN0992.1	EVX1::ELF1	HOX,Ets-related
UN1014.1	FOXI1::ELF1	FOX,Ets-related
UN1020.1	FOXK2::ELF1	FOX,Ets-related
UN1154.1	CREB1::ELF1	CREB-related factors,Ets-related

JASPAR matrix evidence (PMIDs): PMID:20517297, PMID:8756667, PMID:31913281

miRNA regulators (miRDB)

Targeting ELF1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 108 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426

Functional genomics

gnomAD constraint: pLI 0.022, LOEUF 0.656, missense Z 1.61 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000239882 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
13:40,933,428–40,941,326	361 / 396.1	0.91	no
13:40,941,327–40,943,101	34 / 76.8	0.44	no
13:40,943,102–40,982,054	232 / 269.2	0.86	no

Literature-anchored findings (GeneRIF, showing 23)

• Includes a comparison of MEF to ELF1. (PMID:10207087)
• transcriptional regulation of the LAT gene, including the discovery that the Ets transcription factor Elf-1 may play a central role in its expression (PMID:16464244)
• These results provide new evidence that Elf-1 is involved in transcriptional activation of hPygo2. (PMID:18314487)
• Elf-1 in combination with Sp1 and GABP reduced FcRgamma promoter activity. (PMID:18378679)
• aberrantly increased PP2A in lupus T cells dephosphorylates Elf-1 at Thr-231, resulting in limited expression and binding of the 98 kDa Elf-1 form to the CD3zeta and FcRgamma promoters. (PMID:18714041)
• The expression levels of both Elf-1 and VEGF were significantly related with tumor differentiation, lymphatic metastasis, clinical stage, and postoperative survival time in non-small cell lung cancer. (PMID:19624906)
• Data show that VEGFR1 promoter binding sites for ELF-1, CREB and EGR-1/3 play a positive role in gene transcription in endothelial cells. (PMID:19822898)
• The expression of Elf-1 and survivin in non-small cell lung cancer is related to differentiation, lymphatic metastasis, clinical stage, and prognosis, and both are positively correlated with microvessel density. (PMID:20346215)
• ETS transcription factor ELF1 is an important positive regulator of MEIS1 expression (PMID:20600580)
• through a genome-wide association in a Hong Kong Chinese cohort and replication in 2 other Asian populations, identified association of ELF1 with systemic lupus erythematosus (PMID:21044949)
• Data suggest that Elf-1 may modulate breast cancer progression to some extent without having an impact on survival of breast cancer patients. (PMID:21811762)
• the results indicate that insufficient O-GlcNAc modification prevents Elf-1-mediated transcriptional repression and thereby upregulates Tollip gene expression in intestinal epithelial cells. (PMID:21867680)
• Expression of FLI-1, ELF-1, and GABP activated the PF4 promoter in HepG2 cells. (PMID:21931859)
• ELF1 binding occurs at both TERT promoter mutations in melanoma in vitro such that increased recruitment of GABP is enabled by the spatial architecture of native and novel ETS motifs in the TERT promoter region. (PMID:26553150)
• ELF-1 binds an important duplicated GGAA cis-acting element at the OAS1 promoter and in cooperation with RB1 and SP1 recruitment contributes to regulation in response to IFN stimulation. (PMID:26643049)
• We demonstrate that expression of ELF1 is impaired in cHL through genetic and epigenetic alterations, and thus, it may represent an additional member of a TF network whose downregulation contributes to the loss of B-cell phenotype of HRS cells. (PMID:30681722)
• ELF1-mediated LUCAT1 promotes choroidal melanoma by modulating RBX1 expression. (PMID:31968402)
• ELF1 activated long non-coding RNA CASC2 inhibits cisplatin resistance of non-small cell lung cancer via the miR-18a/IRF-2 signaling pathway. (PMID:32271431)
• Transcriptomic Analysis of Naive Human Embryonic Stem Cells Cultured in Three-Dimensional PEG Scaffolds. (PMID:33379237)
• ELF1 Transcription Factor Enhances the Progression of Glioma via ATF5 promoter. (PMID:33720698)
• Transcription Factor ELF1 Modulates Cisplatin Sensitivity in Prostate Cancer by Targeting MEIS Homeobox 2. (PMID:36763086)
• ELF1 suppresses autophagy to reduce cisplatin resistance via the miR-152-3p/NCAM1/ERK axis in lung cancer cells. (PMID:36846943)
• ELF1/PRR11/ARP2/3 promoted trophoblast cells proliferation and motility in early pregnancy. (PMID:37641376)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Elf1	ENSMUSG00000036461
rattus_norvegicus	Elf1	ENSRNOG00000011762

Paralogs (28): ETV1 (ENSG00000006468), ETV7 (ENSG00000010030), SPI1 (ENSG00000066336), ELF4 (ENSG00000102034), ETV2 (ENSG00000105672), ERF (ENSG00000105722), ELF2 (ENSG00000109381), ELK3 (ENSG00000111145), ETV3 (ENSG00000117036), SPDEF (ENSG00000124664), ELK1 (ENSG00000126767), ETS1 (ENSG00000134954), EHF (ENSG00000135373), ELF5 (ENSG00000135374), ETV6 (ENSG00000139083), FLI1 (ENSG00000151702), GABPA (ENSG00000154727), ERG (ENSG00000157554), ETS2 (ENSG00000157557), ELK4 (ENSG00000158711), ELF3 (ENSG00000163435), FEV (ENSG00000163497), SPIC (ENSG00000166211), ETV4 (ENSG00000175832), ETV5 (ENSG00000244405), ETV3L (ENSG00000253831), ERFL (ENSG00000268041), SPIB (ENSG00000269404)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:107180) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal B cell differentiation	1
abnormal B cell physiology	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Drosophila melanogaster	P11536	99.8%	Diamond
Pan paniscus	A1YG61	99.7%	Diamond
Pan troglodytes	A2T737	99.7%	Diamond
Gorilla gorilla gorilla	A1YF15	99.6%	Diamond
Gallus gallus	P13474	99.5%	Diamond
Xenopus laevis	P18755	98.5%	Diamond
Bos taurus	Q2KIC2	98.1%	Diamond
Ateles geoffroyi	A2D4Z7	97.5%	Diamond
Lytechinus variegatus	P29773	93.8%	Diamond
Caenorhabditis elegans	Q18579	87.2%	Diamond
Danio rerio	Q9PUQ1	82.7%	Diamond
Drosophila virilis	Q7M3M6	79.6%	Diamond
Avian leukemia virus e26	P01105	99.4%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
TRE-TTC1-2	tRNA	100189333
WBP4	protein-coding	11193
MIR3168	ncRNA	100422878
KBTBD6	protein-coding	89890
MIR320D1	ncRNA	100313896
SLC25A15	protein-coding	10166
MRPS31	protein-coding	10240
MIR621	ncRNA	693206

Protein

Protein identifiers

ETS-related transcription factor Elf-1 — P32519 (reviewed: P32519)

Alternative names: E74-like factor 1

All UniProt accessions (4): A0A0D9SG85, A0A0U1RRL5, P32519, Q5T9E7

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that activates the LYN and BLK promoters. Appears to be required for the T-cell-receptor-mediated trans activation of HIV-2 gene expression. Binds specifically to two purine-rich motifs in the HIV-2 enhancer.

Subunit / interactions. Binds to the underphosphorylated form of RB. May interact with other transcription factors in order to regulate specific genes. Interacts with RUNX1.

Subcellular location. Nucleus.

Tissue specificity. In fetal tissues, it is highly expressed in heart, lung liver and kidney, and weakly expressed in brain. In adult, it is highly expressed in pancreas, spleen, thymus and peripheral blood leukocytes, expressed at moderate levels in heart, placenta, lung, liver, skeletal muscle, kidney, prostate, ovary, small intestine and colon, and weakly expressed in brain and testis.

Similarity. Belongs to the ETS family.

Isoforms (2)

UniProt ID	Names	Canonical?
P32519-1	1	yes
P32519-2	2

RefSeq proteins (6): NP_001138825, NP_001357258, NP_001357259, NP_001357260, NP_001357261, NP_758961* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000418	Ets_dom	Domain
IPR022084	TF_Elf_N	Domain
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR046328	ETS_fam	Family

Pfam: PF00178, PF12310

UniProt features (29 total): modified residue 7, helix 5, compositionally biased region 4, sequence variant 3, region of interest 3, strand 3, chain 1, DNA-binding region 1, splice variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
8BZM	FOXK1-ELF1-heterodimer bound to DNA	X-RAY DIFFRACTION	2.69

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P32519-F1	53.55	0.13

Human Protein Atlas

Protein class: Predicted intracellular proteins, Transcription factors, Helix-turn-helix domains

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (7)

Type	Positions
Phosphoserine	163, 167, 168, 187, 432, 110
Phosphothreonine	190

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 6; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

6 pathways:

ID	Pathway	Evidence
R-HSA-8939245	RUNX1 regulates transcription of genes involved in BCR signaling	curated
R-HSA-8939247	RUNX1 regulates transcription of genes involved in interleukin signaling	curated
R-HSA-74160	Gene expression (Transcription)	—
R-HSA-212436	Generic Transcription Pathway	—
R-HSA-73857	RNA Polymerase II Transcription	—
R-HSA-8878171	Transcriptional regulation by RUNX1	—

MSigDB gene sets: 0 (showing top):

GO Biological Process (6): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), cell differentiation (GO:0030154), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

4 top-level categories:

Category	Pathways
Transcriptional regulation by RUNX1	2
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1
Generic Transcription Pathway	1

GO top-level categories

29 GO namespaces:

Category	Terms
regulation of DNA-templated transcription	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
DNA-templated transcription	2
regulation of transcription by RNA polymerase II	2
cellular anatomical structure	2
gene expression	1
RNA biosynthetic process	1
cellular developmental process	1
positive regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
DNA binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 8 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

8 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of DNA-templated transcription	BP	direct assay
positive regulation of transcription by RNA polymerase II	BP	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay
DNA-binding transcription activator activity, RNA polymerase II-specific	MF	direct assay
DNA-binding transcription factor activity	MF	direct assay
RNA polymerase II cis-regulatory region sequence-specific DNA binding	MF	direct assay
sequence-specific double-stranded DNA binding	MF	direct assay

Protein interactions and networks

STRING

showing 16 of 822 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ELF1	EPHA1	P21709	660
ELF1	GABPA	Q06546	499
ELF1	BLZF1	Q9H2G9	427
ELF1	BACH1	O14867	370
ELF1	GUF1	Q8N442	368
ELF1	LRRC30	A6NM36	360
ELF1	EEF1D	P29692	360
ELF1	RFX5	P48382	358
ELF1	ETS1	P14921	324
ELF1	GABPB1	Q06547	311
ELF1	ZCCHC3	Q9NUD5	308
ELF1	ATE1	O95260	302
ELF1	FLRT1	Q9NZU1	300
ELF1	MED23	Q9ULK4	287
ELF1	WDR64	B1ANS9	261
ELF1	LMO2	P25791	261

IntAct

Human interaction partners of ELF1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

9 partners by confidence:

Partner	Interaction type	MIscore	Records
NFYC	physical association	0.560	3
HSPBP1	physical association	0.560	1
HOXC13	physical association	0.520	3
SP1	physical association	0.510	2
HNRNPUL1	physical association	0.400	1
E7	physical association	0.370	1
NFE2L2	physical association	0.370	1
KLHL6	association	0.350	1
SMCHD1	proximity	0.270	1

BioGRID (130 interactions; top human partners by supporting records): HOXC13 (Affinity Capture-Western; 2 records), HSPBP1 (Affinity Capture-MS; 2 records), NFIA (Proximity Label-MS; 2 records), NFIX (Proximity Label-MS; 2 records), NFKB1 (Reconstituted Complex; 2 records), ACTR5 (Proximity Label-MS), ACTR6 (Proximity Label-MS), ARID2 (Proximity Label-MS), ARID4B (Proximity Label-MS), ARL2BP (Affinity Capture-MS), ASH2L (Proximity Label-MS), ASXL2 (Proximity Label-MS), ATF1 (Proximity Label-MS), ATXN1L (Proximity Label-MS), BAP1 (Proximity Label-MS)

SIGNOR signaling

5 signaling interactions:

A	Effect	B	Mechanism
ELF1	“up-regulates quantity by expression”	IL2RA	“transcriptional regulation”
PPP2CB	“down-regulates activity”	ELF1	dephosphorylation
PPP2CA	“down-regulates activity”	ELF1	dephosphorylation
ELF1	“down-regulates quantity by repression”	FCER1A	“transcriptional regulation”
ELF1	“up-regulates quantity by expression”	CD68	“transcriptional regulation”

Disease & clinical

Genetic variants

Variant evidence for ELF1: 97 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

97 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	1
Benign	2

AlphaMissense

963 missense substitutions predicted likely pathogenic (of 4,035 scored), across 218 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M259	9	0.998	1.000
M264	9	0.992	1.000
F238	8	1.000	1.000
F289	8	0.998	1.000
F213	8	0.994	1.000
N260	8	0.992	1.000
D242	8	0.977	0.999
D220	8	0.975	0.997
N255	8	0.972	0.998
D258	8	0.954	0.993
H253	8	0.895	0.998
W211	7	1.000	1.000
W230	7	1.000	1.000
W250	7	1.000	1.000
E262	7	1.000	1.000
R269	7	0.999	1.000
R274	7	0.989	1.000
K279	7	0.989	1.000
I276	7	0.988	1.000
C224	7	0.987	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	3.27e-10
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	6.88e-05

Disease associations

OMIM: gene MIM:189973 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

56 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
trichostatin A	affects cotreatment, increases expression	3
Panobinostat	affects cotreatment, increases expression	2
Estradiol	increases expression, affects expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
FR900359	increases phosphorylation	1
testosterone enanthate	affects expression	1
methylmercuric chloride	increases expression	1
geraniol	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	decreases expression	1
manganese chloride	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	increases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
clothianidin	increases expression	1
torcetrapib	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Arsenic Trioxide	affects methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1

Cellosaurus cell lines

5 cell lines: 3 embryonic stem cell, 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A1G6	SEES3-1V human ELF1, clone1	Embryonic stem cell	Male
CVCL_A1G7	SEES3-1V human ELF1, clone2	Embryonic stem cell	Male
CVCL_A1G8	SEES3-1V human ELF1, clone3	Embryonic stem cell	Male
CVCL_GZ81	K562 eGFP-ELF1	Cancer cell line	Female
CVCL_HA13	MCF-7 eGFP-ELF1	Cancer cell line	Female

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.