UBTFL1

Summary

UBTFL1 (upstream binding transcription factor like 1, HGNC:14533) is a protein-coding gene on chromosome 11q14.3, encoding Upstream-binding factor 1-like protein 1 (P0CB47). Essential for proliferation of the inner cell mass and trophectodermal cells in peri-implantation development.

Predicted to enable RNA polymerase I core promoter sequence-specific DNA binding activity and RNA polymerase I general transcription initiation factor activity. Predicted to be involved in positive regulation of transcription by RNA polymerase I and transcription by RNA polymerase I. Predicted to act upstream of or within blastocyst growth; embryo implantation; and regulation of gene expression. Predicted to be located in cytoplasm and intracellular membrane-bounded organelle. Predicted to be active in nucleus.

Source: NCBI Gene 642623 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_001143975

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14533
Approved symbol	UBTFL1
Name	upstream binding transcription factor like 1
Location	11q14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000255009
Ensembl biotype	protein_coding
OMIM	613696
Entrez	642623

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000530464

RefSeq mRNA: 1 — MANE Select: NM_001143975 NM_001143975

CCDS: CCDS44704

Canonical transcript exons

ENST00000530464 — 1 exons

Exon	Start	End
ENSE00002143242	90085950	90087131

Expression profiles

Bgee: expression breadth tissue_specific, 5 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.78	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
urinary bladder	UBERON:0001255	30.28	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
lymph node	UBERON:0000029	29.42	silver quality
prefrontal cortex	UBERON:0000451	29.21	gold quality
liver	UBERON:0002107	28.59	gold quality
pituitary gland	UBERON:0000007	28.56	silver quality
monocyte	CL:0000576	28.29	gold quality
leukocyte	CL:0000738	28.23	gold quality
duodenum	UBERON:0002114	28.14	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
blood	UBERON:0000178	26.44	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
frontal cortex	UBERON:0001870	24.26	gold quality
pancreas	UBERON:0001264	24.13	gold quality
superior frontal gyrus	UBERON:0002661	24.08	gold quality
gastrocnemius	UBERON:0001388	23.71	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Functionally characterizes an homologous mouse gene and product, and compares it to this human product. (PMID:19915186)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubtf	ENSDARG00000035066
danio_rerio	ubtfl	ENSDARG00000038780
mus_musculus	Ubtfl1	ENSMUSG00000074502
rattus_norvegicus	Ubtfl1	ENSRNOG00000079909
rattus_norvegicus		ENSRNOG00000084112
caenorhabditis_elegans	hmg-3	WBGENE00001973
caenorhabditis_elegans		WBGENE00001974

Paralogs (20): HMGB3 (ENSG00000029993), HMG20B (ENSG00000064961), SP100 (ENSG00000067066), SMARCE1 (ENSG00000073584), SP140 (ENSG00000079263), TOX4 (ENSG00000092203), HMGXB4 (ENSG00000100281), TOX3 (ENSG00000103460), TFAM (ENSG00000108064), UBTF (ENSG00000108312), HMGB1P1 (ENSG00000124097), TOX2 (ENSG00000124191), SP110 (ENSG00000135899), HMG20A (ENSG00000140382), SSRP1 (ENSG00000149136), HMGB2 (ENSG00000164104), HMGB4 (ENSG00000176256), SP140L (ENSG00000185404), HMGB1 (ENSG00000189403), TOX (ENSG00000198846)

Protein

Protein identifiers

Upstream-binding factor 1-like protein 1 — P0CB47 (reviewed: P0CB47)

All UniProt accessions (1): P0CB47

UniProt curated annotations — full annotation on UniProt →

Function. Essential for proliferation of the inner cell mass and trophectodermal cells in peri-implantation development.

Subcellular location. Cytoplasm. Nucleus.

RefSeq proteins (1): NP_001137447* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009071	HMG_box_dom	Domain
IPR036910	HMG_box_dom_sf	Homologous_superfamily
IPR051762	UBF1	Family

Pfam: PF00505

UniProt features (5 total): DNA-binding region 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CB47-F1	71.73	0.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_GROWTH, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_BLASTOCYST_DEVELOPMENT, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GOBP_EMBRYO_DEVELOPMENT, GOBP_BLASTOCYST_GROWTH, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_DEVELOPMENTAL_GROWTH, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_CORE_PROMOTER_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_RNA_POLYMERASE_I_PREINITIATION_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_I, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_I

GO Biological Process (6): blastocyst growth (GO:0001832), transcription by RNA polymerase I (GO:0006360), embryo implantation (GO:0007566), positive regulation of transcription by RNA polymerase I (GO:0045943), RNA polymerase I preinitiation complex assembly (GO:0001188), regulation of gene expression (GO:0010468)

GO Molecular Function (4): RNA polymerase I core promoter sequence-specific DNA binding (GO:0001164), RNA polymerase I general transcription initiation factor activity (GO:0001181), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase I	2
blastocyst development	1
developmental growth	1
DNA-templated transcription	1
multicellular organism development	1
female pregnancy	1
reproductive process	1
regulation of transcription by RNA polymerase I	1
positive regulation of DNA-templated transcription	1
transcription initiation at RNA polymerase I promoter	1
transcription preinitiation complex assembly	1
gene expression	1
regulation of macromolecule biosynthetic process	1
core promoter sequence-specific DNA binding	1
RNA polymerase I transcription regulatory region sequence-specific DNA binding	1
RNA polymerase I preinitiation complex assembly	1
general transcription initiation factor activity	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

844 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBTFL1	BDP1	A6H8Y1	761
UBTFL1	ZSCAN4	Q8NAM6	624
UBTFL1	CDX2	Q99626	617
UBTFL1	NANOG	Q9H9S0	578
UBTFL1	POU5F1	P31359	556
UBTFL1	SERBP1	Q8NC51	500
UBTFL1	SP140	Q13342	492
UBTFL1	OR2T2	Q6IF00	445
UBTFL1	NCOR1	O75376	431
UBTFL1	ZNF736	B4DX44	420
UBTFL1	OR4C3	Q8NH37	400
UBTFL1	ZSCAN5C	A6NGD5	372
UBTFL1	MSX2	P35548	353
UBTFL1	OR1E2	P47887	353
UBTFL1	DISP1	Q96F81	353
UBTFL1	IL17RC	Q8NAC3	353
UBTFL1	TCF7	P36402	353
UBTFL1	TACC2	O95359	353

IntAct

85 interactions, top by confidence:

A	B	Type	Score
UBTFL1	CDR2	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	NACC1	psi-mi:“MI:0915”(physical association)	0.560
ZBTB7B	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.560
	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	RUNDC3A	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	STX1A	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	LBX1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	PUF60	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	LHX9	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	LHX3	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	RABEP1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	BEND3	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	TAX1BP1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	LHX2	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
LDOC1	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	OR4F3	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	OR5AS1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	DDIT4L	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	C3orf36	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	ZNF558	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	PBX4	psi-mi:“MI:0915”(physical association)	0.560
FSD2	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
NOTO	UBTFL1	psi-mi:“MI:0915”(physical association)	0.560
UBTFL1	CDR2	psi-mi:“MI:0915”(physical association)	0.000
UBTFL1	NACC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (30): UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid), UBTFL1 (Two-hybrid)

ESM2 similar proteins: A2CG63, C0SUW7, F4JQZ3, F8VPQ2, I1HNB2, O49595, O49597, O64702, O70523, O75400, O96028, P0CB47, P0CB48, P17480, P25976, P25977, P25979, P25980, P26585, P29374, P40620, P40630, P51115, P93831, Q02395, Q0WNR6, Q3USZ2, Q42344, Q5BJ56, Q5R7T9, Q5VN06, Q5ZKF4, Q61584, Q6AZF8, Q6DIJ5, Q6INA9, Q8BVE8, Q8LA53, Q8LDF9, Q8LPQ7

Diamond homologs: P0CB47, P0CB48, P17480, P25976, P25977, P25979, P25980, P40626, Q0II87, Q3USZ2, Q5D144, P11873, P40625, Q02486, Q32L68, Q4IQX3, Q5ZKF4, Q7S045, Q9P0W2, Q9Z104, B2RPK0, B3DLD3, C7U331, O04235, O49596, O54879, O60248, O64702, P07156, P07746, P0CY16, P0CY17, P11633, P26585, P33417, P35713, P40619, P40620, P40621, P40622

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

178 predictions. Top by Δscore:

Variant	Effect	Δscore
11:90087034:T:TA	acceptor_gain	0.8800
11:90087035:G:A	acceptor_gain	0.6300
11:90087034:T:G	acceptor_gain	0.6200
11:90087033:AT:A	acceptor_gain	0.5900
11:90086661:TC:T	donor_gain	0.5700
11:90086589:A:T	donor_gain	0.5500
11:90087042:GAAGA:G	acceptor_gain	0.5400
11:90087041:A:AG	acceptor_gain	0.5300
11:90087042:G:GG	acceptor_gain	0.5300
11:90087072:G:GT	donor_gain	0.5300
11:90087042:GAA:G	acceptor_gain	0.5200
11:90086766:GC:G	donor_gain	0.5100
11:90087033:A:AG	acceptor_gain	0.5100
11:90087033:ATG:A	acceptor_gain	0.5100
11:90086454:G:T	donor_gain	0.4900
11:90086585:CAAGA:C	acceptor_gain	0.4900
11:90086586:AAGAA:A	acceptor_gain	0.4900
11:90087026:T:G	acceptor_gain	0.4900
11:90087021:T:A	acceptor_gain	0.4800
11:90087038:A:AG	acceptor_gain	0.4800
11:90087019:A:AG	acceptor_gain	0.4700
11:90086587:AGAAG:A	donor_loss	0.4600
11:90086589:AAGGT:A	donor_loss	0.4600
11:90086590:AG:A	donor_loss	0.4600
11:90086591:GGTAA:G	donor_loss	0.4600
11:90086592:G:A	donor_loss	0.4600
11:90086593:T:G	donor_loss	0.4600
11:90086867:GG:G	donor_gain	0.4500
11:90086868:GG:G	donor_gain	0.4500
11:90087018:AACT:A	donor_gain	0.4500

AlphaMissense

2645 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:90086643:T:C	F232L	0.979
11:90086645:T:A	F232L	0.979
11:90086645:T:G	F232L	0.979
11:90086808:T:A	W287R	0.976
11:90086808:T:C	W287R	0.976
11:90086277:T:C	F110L	0.975
11:90086279:C:A	F110L	0.975
11:90086279:C:G	F110L	0.975
11:90086721:T:A	W258R	0.972
11:90086721:T:C	W258R	0.972
11:90086723:G:C	W258C	0.969
11:90086723:G:T	W258C	0.969
11:90086810:G:C	W287C	0.969
11:90086810:G:T	W287C	0.969
11:90086091:T:C	F48L	0.964
11:90086093:T:A	F48L	0.964
11:90086093:T:G	F48L	0.964
11:90086747:G:C	K266N	0.962
11:90086747:G:T	K266N	0.962
11:90086809:G:C	W287S	0.962
11:90086698:G:C	R250P	0.961
11:90086722:G:C	W258S	0.958
11:90086127:T:A	W60R	0.956
11:90086127:T:C	W60R	0.956
11:90086275:G:C	R109P	0.955
11:90086644:T:C	F232S	0.955
11:90086787:T:G	Y280D	0.950
11:90086610:C:T	P221S	0.948
11:90086387:A:C	K146N	0.947
11:90086387:A:T	K146N	0.947

dbSNP variants (sampled 300 via entrez): RS1007646169 (11:90084137 C>A,T), RS1008031751 (11:90084719 G>C,T), RS1010899223 (11:90084809 A>C), RS1011347567 (11:90084315 C>T), RS1012745638 (11:90085460 G>T), RS1013254966 (11:90086468 T>C,G), RS1017990284 (11:90084187 C>T), RS1019029543 (11:90086985 G>A,C,T), RS1021003577 (11:90084820 A>C), RS1021538880 (11:90084316 T>C), RS1022766124 (11:90086632 G>C), RS1023261706 (11:90085498 A>C), RS1025909437 (11:90085734 G>T), RS1026004561 (11:90086943 G>C), RS1035492028 (11:90084919 T>C)

Disease associations

OMIM: gene MIM:613696 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST012020_223	Serum metabolite levels	2.000000e-29
GCST012020_224	Serum metabolite levels	2.000000e-47

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1

Clinical trials (associated diseases)

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