ELOF1

Summary

ELOF1 (elongation factor 1, HGNC:28691) is a protein-coding gene on chromosome 19p13.2, encoding Transcription elongation factor 1 homolog (P60002). Factor involved in transcription-coupled nucleotide excision repair (TC-NER), a mechanism that rapidly removes RNA polymerase II-blocking lesions from the transcribed strand of active genes.

Predicted to enable RNA polymerase II complex binding activity. Predicted to be involved in transcription elongation by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of transcription elongation factor complex.

Source: NCBI Gene 84337 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_032377

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28691
Approved symbol	ELOF1
Name	elongation factor 1
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC4549, ELF1
Ensembl gene	ENSG00000130165
Ensembl biotype	protein_coding
OMIM	619818
Entrez	84337

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 31 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000252445, ENST00000586120, ENST00000586683, ENST00000587806, ENST00000589171, ENST00000590700, ENST00000591674, ENST00000591912, ENST00000593077, ENST00000890143, ENST00000890144, ENST00000890145, ENST00000890146, ENST00000890147, ENST00000890148, ENST00000890149, ENST00000890150, ENST00000890151, ENST00000890152, ENST00000921351, ENST00000921352, ENST00000921353, ENST00000921354, ENST00000921355, ENST00000921356, ENST00000921357, ENST00000921358, ENST00000921359, ENST00000947485, ENST00000947486, ENST00000947487, ENST00000947488

RefSeq mRNA: 4 — MANE Select: NM_032377 NM_001363673, NM_001363674, NM_001363675, NM_032377

CCDS: CCDS12264

Canonical transcript exons

ENST00000252445 — 4 exons

Exon	Start	End
ENSE00000894046	11554011	11554081
ENSE00001061357	11553046	11553810
ENSE00002753686	11559191	11559230
ENSE00003469475	11554232	11554365

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 98.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.1540 / max 294.9251, expressed in 1822 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179254	33.7695	1822
179256	0.2342	33
179255	0.1503	34

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.87	gold quality
right testis	UBERON:0004534	98.82	gold quality
tendon of biceps brachii	UBERON:0008188	98.31	gold quality
pancreatic ductal cell	CL:0002079	96.94	silver quality
testis	UBERON:0000473	96.49	gold quality
adenohypophysis	UBERON:0002196	96.20	gold quality
body of pancreas	UBERON:0001150	95.91	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.78	gold quality
cerebellar hemisphere	UBERON:0002245	95.70	gold quality
cerebellar cortex	UBERON:0002129	95.66	gold quality
sperm	CL:0000019	95.64	gold quality
body of uterus	UBERON:0009853	95.60	gold quality
right uterine tube	UBERON:0001302	95.48	gold quality
body of stomach	UBERON:0001161	95.39	gold quality
pituitary gland	UBERON:0000007	95.38	gold quality
granulocyte	CL:0000094	95.35	gold quality
right frontal lobe	UBERON:0002810	95.23	gold quality
left uterine tube	UBERON:0001303	95.15	gold quality
hypothalamus	UBERON:0001898	95.15	gold quality
anterior cingulate cortex	UBERON:0009835	95.05	gold quality
mucosa of transverse colon	UBERON:0004991	94.97	gold quality
cerebellum	UBERON:0002037	94.96	gold quality
endocervix	UBERON:0000458	94.91	gold quality
left adrenal gland	UBERON:0001234	94.58	gold quality
left adrenal gland cortex	UBERON:0035825	94.58	gold quality
right ovary	UBERON:0002118	94.55	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.51	gold quality
upper arm skin	UBERON:0004263	94.50	silver quality
amygdala	UBERON:0001876	94.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.45	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting ELOF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-516A-3P	99.46	67.96	1378
HSA-MIR-516B-3P	99.46	67.96	1378
HSA-MIR-7162-5P	99.46	68.08	1368
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-6780B-3P	99.13	67.18	622
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-4724-5P	98.87	67.75	1324
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-3158-3P	98.45	64.25	560
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-7114-3P	98.42	66.53	569
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-4308	97.56	67.13	1385
HSA-MIR-409-5P	97.31	68.07	364
HSA-MIR-6849-3P	97.25	64.57	1371

Literature-anchored findings (GeneRIF, showing 2)

• Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. (PMID:34108662)
• ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. (PMID:34108663)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	elof1	ENSDARG00000099453
mus_musculus	Elof1	ENSMUSG00000013822
rattus_norvegicus	Elof1	ENSRNOG00000014284
drosophila_melanogaster	CG40228	FBGN0063670
caenorhabditis_elegans		WBGENE00013219

Protein

Protein identifiers

Transcription elongation factor 1 homolog — P60002 (reviewed: P60002)

All UniProt accessions (6): P60002, A0A024R7E8, K7EMV4, K7EN05, K7EPC8, K7EQ44

UniProt curated annotations — full annotation on UniProt →

Function. Factor involved in transcription-coupled nucleotide excision repair (TC-NER), a mechanism that rapidly removes RNA polymerase II-blocking lesions from the transcribed strand of active genes. Acts as a key adapter required to anchor TC-NER factors to RNA polymerase II: stably positions UVSSA and the DCX(ERCC8) complex (also named CSA complex) on arrested RNA polymerase II, leading to neddylation and activation of the DCX(ERCC8) complex and ubiquitination of RNA polymerase II.

Subunit / interactions. Associates with RNA polymerase II.

Subcellular location. Nucleus. Chromosome.

Similarity. Belongs to the ELOF1 family.

RefSeq proteins (4): NP_001350602, NP_001350603, NP_001350604, NP_115753* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007808	Elf1	Family
IPR038567	T_Elf1_sf	Homologous_superfamily

Pfam: PF05129

UniProt features (17 total): binding site 4, strand 4, mutagenesis site 4, turn 3, chain 1, helix 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
9MLC	ELECTRON MICROSCOPY	2.4
8B3D	ELECTRON MICROSCOPY	2.6
8XRM	ELECTRON MICROSCOPY	3.13
9ER2	ELECTRON MICROSCOPY	3.3
9FD2	ELECTRON MICROSCOPY	3.4
9RTT	ELECTRON MICROSCOPY	4.01

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P60002-F1	85.98	0.69

Functional residue map

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

Ligand- & substrate-binding residues (4): 26; 29; 50; 53

Mutagenesis-validated functional residues (4):

Position	Phenotype
30–32	abolished interaction with the dcx(ercc8) complex, leading to defects in transcription-coupled nucleotide excision repai
55	does not affect transcription-coupled nucleotide excision repair (tc-ner); when associated with a-79.
72–73	reduced interaction with rna polymerase ii.
79	does not affect transcription-coupled nucleotide excision repair (tc-ner); when associated with a-55.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): PAL_PRMT5_TARGETS_UP, TTTGTAG_MIR520D, GOBP_TRANSCRIPTION_COUPLED_NUCLEOTIDE_EXCISION_REPAIR, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CACCAGC_MIR138, GOBP_NUCLEOTIDE_EXCISION_REPAIR, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, ACATTCC_MIR1_MIR206, GOBP_DNA_DAMAGE_RESPONSE, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, TGACATY_UNKNOWN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, TCCAGAG_MIR518C, WGGAATGY_TEF1_Q6, GOCC_TRANSCRIPTION_ELONGATION_FACTOR_COMPLEX

GO Biological Process (5): transcription-coupled nucleotide-excision repair (GO:0006283), transcription elongation by RNA polymerase II (GO:0006368), DNA repair (GO:0006281), translational elongation (GO:0006414), DNA damage response (GO:0006974)

GO Molecular Function (4): RNA polymerase II complex binding (GO:0000993), protein-macromolecule adaptor activity (GO:0030674), translation elongation factor activity (GO:0003746), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), chromosome (GO:0005694), transcription elongation factor complex (GO:0008023)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleotide-excision repair	1
DNA-templated transcription elongation	1
transcription by RNA polymerase II	1
DNA metabolic process	1
DNA damage response	1
translation	1
macromolecule biosynthetic process	1
cellular response to stress	1
RNA polymerase core enzyme binding	1
protein binding	1
molecular adaptor activity	1
translational elongation	1
translation factor activity	1
binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
nucleoplasm	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

1176 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ELOF1	UVSSA	Q2YD98	657
ELOF1	MICOS10	Q5TGZ0	587
ELOF1	ERCC6L2	Q5T890	568
ELOF1	GTF2H1	P32780	558
ELOF1	MRPL48	Q96GC5	547
ELOF1	SUPT5H	O00267	545
ELOF1	GCSH	P23434	539
ELOF1	COX7A2	P14406	528
ELOF1	ZSWIM7	Q19AV6	528
ELOF1	GUK1	Q16774	511
ELOF1	ANAPC11	Q9NYG5	509
ELOF1	COX5B	P10606	507
ELOF1	SCAF4	O95104	482
ELOF1	TCEA3	O75764	482
ELOF1	ATP6V1F	Q16864	480

IntAct

13 interactions, top by confidence:

A	B	Type	Score
ELOF1	C5orf22	psi-mi:“MI:0915”(physical association)	0.670
C5orf22	ELOF1	psi-mi:“MI:0915”(physical association)	0.670
ELOF1	CHMP6	psi-mi:“MI:0915”(physical association)	0.370
ELOF1	MAPK6	psi-mi:“MI:0915”(physical association)	0.370
ELOF1	SUV39H1	psi-mi:“MI:0915”(physical association)	0.370
ELOF1	KDM1A	psi-mi:“MI:0915”(physical association)	0.370
	EBAG9	psi-mi:“MI:0914”(association)	0.350
C5orf22	ELOF1	psi-mi:“MI:0915”(physical association)	0.000
ATP5F1C	ELOF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (75): ELOF1 (Two-hybrid), ELOF1 (Affinity Capture-MS), ELOF1 (Affinity Capture-MS), ELOF1 (Biochemical Activity), ELOF1 (Two-hybrid), ELOF1 (Two-hybrid), ELOF1 (Positive Genetic), ELOF1 (Negative Genetic), POLR2C (Affinity Capture-MS), POLR2J (Affinity Capture-MS), POLR2H (Affinity Capture-MS), POLR2E (Affinity Capture-MS), POLR2D (Affinity Capture-MS), POLR2L (Affinity Capture-MS), POLR2A (Affinity Capture-MS)

ESM2 similar proteins: A2XIP9, A4IFR3, O13868, O13896, O24473, O74635, P10711, P23193, P27999, P37164, P37165, P38861, P48598, P53803, P60002, P60003, Q08DS5, Q09817, Q0VA16, Q148K0, Q15560, Q21230, Q29RL9, Q2M2S7, Q32LB0, Q3TWF6, Q3ZBC0, Q4KLL0, Q54KR5, Q5EB92, Q5RC82, Q63871, Q6FS48, Q6GPP0, Q6MFY5, Q755B3, Q75LU5, Q791N7, Q8LEF3, Q8LHP0

Diamond homologs: A4IFR3, O13868, P36053, P60002, P60003, Q54KR5, Q8LEF3, Q8LHP0, Q8MQI6, Q9U501, Q9XVZ8, Q8STS7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SMURF1	unknown	ELOF1	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3229 predictions. Top by Δscore:

Variant	Effect	Δscore
13:40934027:TCCT:T	acceptor_loss	1.0000
13:40934029:C:CA	acceptor_loss	1.0000
13:40934030:T:G	acceptor_loss	1.0000
13:40943837:AGTAC:A	donor_gain	1.0000
13:40943840:AC:A	donor_gain	1.0000
13:40943841:CC:C	donor_gain	1.0000
13:40943846:T:A	donor_gain	1.0000
13:40949802:CTA:C	donor_loss	1.0000
13:40949803:TA:T	donor_loss	1.0000
13:40951323:A:AC	donor_gain	1.0000
13:40951324:C:CC	donor_gain	1.0000
13:40951324:CTCA:C	donor_gain	1.0000
13:40951325:TCACT:T	donor_loss	1.0000
13:40951326:CACT:C	donor_loss	1.0000
13:40951327:A:AC	donor_gain	1.0000
13:40951328:C:CA	donor_gain	1.0000
13:40951328:CT:C	donor_gain	1.0000
13:40951328:CTT:C	donor_gain	1.0000
13:40951328:CTTA:C	donor_gain	1.0000
13:40951328:CTTAT:C	donor_gain	1.0000
13:40951331:A:AC	donor_gain	1.0000
13:40951331:ATT:A	donor_gain	1.0000
13:40951332:T:C	donor_gain	1.0000
13:40951432:TTCAA:T	acceptor_gain	1.0000
13:40951433:TCAA:T	acceptor_gain	1.0000
13:40951434:CAA:C	acceptor_gain	1.0000
13:40951434:CAAC:C	acceptor_gain	1.0000
13:40951435:AA:A	acceptor_gain	1.0000
13:40951437:C:CC	acceptor_gain	1.0000
13:40951438:T:A	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000435653 (19:11553497 G>C), RS1000975716 (19:11556036 G>A), RS1001111561 (19:11555867 C>G,T), RS1001559874 (19:11559009 A>C), RS1001742119 (19:11552903 G>A,T), RS1001910360 (19:11557587 C>T), RS1001971697 (19:11557757 G>C), RS1002227057 (19:11559050 G>A), RS1002830558 (19:11560236 G>C), RS1002960474 (19:11559903 C>T), RS1004340385 (19:11556805 C>T), RS1005060035 (19:11555220 G>A), RS1005346340 (19:11558601 T>C), RS1005445503 (19:11560886 T>A,C), RS1005733392 (19:11558302 G>C,T)

Disease associations

OMIM: gene MIM:619818 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation	2
aristolochic acid I	increases expression	1
ginger extract	increases expression, decreases reaction, increases abundance	1
bisphenol A	increases expression, decreases reaction, increases abundance	1
trichostatin A	affects expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	affects cotreatment, increases expression	1
aflatoxin B2	increases methylation	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Cadmium	increases expression, increases abundance	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Methapyrilene	increases methylation	1
Oils, Volatile	decreases reaction, increases abundance, increases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2WI	Abcam HEK293T ELOF1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.