SSU72L3

Summary

SSU72L3 (SSU72 like 3, HGNC:43622) is a protein-coding gene on chromosome 11p15.4, encoding RNA polymerase II subunit A C-terminal domain phosphatase SSU72 like protein 3 (A0A1W2PQJ5). Protein phosphatase that catalyzes the dephosphorylation of the C-terminal domain of RNA polymerase II.

Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in termination of RNA polymerase II transcription. Predicted to be located in nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex.

Source: NCBI Gene 143506 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001414000

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43622
Approved symbol	SSU72L3
Name	SSU72 like 3
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000284546
Ensembl biotype	protein_coding
Entrez	143506

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000640302

RefSeq mRNA: 1 — MANE Select: NM_001414000 NM_001414000

Canonical transcript exons

ENST00000640302 — 1 exons

Exon	Start	End
ENSE00002161169	4329790	4330864

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 37.20.

Top tissues by expression

111 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
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	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
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
gall bladder	UBERON:0002110	28.91	silver quality
monocyte	CL:0000576	28.39	gold quality
placenta	UBERON:0001987	28.37	silver quality
leukocyte	CL:0000738	28.32	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
rectum	UBERON:0001052	25.67	gold quality
endometrium	UBERON:0001295	24.96	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
pancreas	UBERON:0001264	24.14	gold quality
superior frontal gyrus	UBERON:0002661	24.08	gold quality
calcaneal tendon	UBERON:0003701	23.08	gold quality
smooth muscle tissue	UBERON:0001135	22.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.97

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ssu72	ENSDARG00000031216
drosophila_melanogaster	Ssu72	FBGN0031054
caenorhabditis_elegans		WBGENE00020480

Paralogs (6): SSU72 (ENSG00000160075), SSU72L6 (ENSG00000230268), SSU72L4 (ENSG00000283873), SSU72L5 (ENSG00000284018), SSU72L2 (ENSG00000284306), SSU72L1 (ENSG00000284438)

Protein

Protein identifiers

RNA polymerase II subunit A C-terminal domain phosphatase SSU72 like protein 3 — A0A1W2PQJ5 (reviewed: A0A1W2PQJ5)

Alternative names: RNA polymerase II subunit A C-terminal domain phosphatase SSU72L3

All UniProt accessions (1): A0A1W2PQJ5

UniProt curated annotations — full annotation on UniProt →

Function. Protein phosphatase that catalyzes the dephosphorylation of the C-terminal domain of RNA polymerase II. Plays a role in RNA processing and termination.

Subcellular location. Nucleus.

Similarity. Belongs to the SSU72 phosphatase family.

RefSeq proteins (1): NP_001400929* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006811	RNA_pol_II_suA	Family
IPR036196	Ptyr_pPase_sf	Homologous_superfamily

Pfam: PF04722

Catalyzed reactions (Rhea), 2 shown:

• O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate (RHEA:20629)
• O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate (RHEA:47004)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PQJ5-F1	94.89	0.90

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GOBP_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION, GOBP_MRNA_3_END_PROCESSING, GOBP_TERMINATION_OF_RNA_POLYMERASE_II_TRANSCRIPTION, GOCC_MRNA_CLEAVAGE_FACTOR_COMPLEX, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_PROTEIN_SERINE_THREONINE_PHOSPHATASE_ACTIVITY, GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY, GOBP_MRNA_PROCESSING, GOMF_PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY, GOMF_RNA_POLYMERASE_II_CTD_HEPTAPEPTIDE_REPEAT_PHOSPHATASE_ACTIVITY, GOMF_PHOSPHATASE_ACTIVITY, GOCC_MRNA_CLEAVAGE_AND_POLYADENYLATION_SPECIFICITY_FACTOR_COMPLEX, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, GOMF_RNA_POLYMERASE_II_CTD_HEPTAPEPTIDE_REPEAT_MODIFYING_ACTIVITY, GOBP_MRNA_METABOLIC_PROCESS

GO Biological Process (4): termination of RNA polymerase II transcription (GO:0006369), mRNA 3’-end processing (GO:0031124), regulation of transcription by RNA polymerase II (GO:0006357), mRNA processing (GO:0006397)

GO Molecular Function (4): RNA polymerase II CTD heptapeptide repeat phosphatase activity (GO:0008420), phosphoprotein phosphatase activity (GO:0004721), protein serine/threonine phosphatase activity (GO:0004722), hydrolase activity (GO:0016787)

GO Cellular Component (2): mRNA cleavage and polyadenylation specificity factor complex (GO:0005847), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	2
DNA-templated transcription termination	1
mRNA processing	1
RNA 3’-end processing	1
regulation of DNA-templated transcription	1
RNA processing	1
mRNA metabolic process	1
protein serine/threonine phosphatase activity	1
RNA polymerase II CTD heptapeptide repeat modifying activity	1
phosphatase activity	1
catalytic activity, acting on a protein	1
phosphoprotein phosphatase activity	1
catalytic activity	1
mRNA cleavage factor complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

374 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSU72L3	SYMPK	Q92797	207
SSU72L3	PCF11	O94913	207
SSU72L3	CSTF3	Q12996	207
SSU72L3	CTDP1	Q9Y5B0	207
SSU72L3	WDR82	Q6UXN9	206
SSU72L3	GTF2B	Q00403	206
SSU72L3	CPSF1	Q10570	206
SSU72L3	CPSF3	Q9UKF6	205
SSU72L3	CPSF2	Q9P2I0	205
SSU72L3	SUPT5H	O00267	205
SSU72L3	PIN1	Q13526	204
SSU72L3	WDR33	Q9C0J8	204
SSU72L3	RPAP2	Q8IXW5	204
SSU72L3	POLR2B	P30876	194
SSU72L3	POLR2A	P24928	188

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1W2PQ27, A0A1W2PQ64, A0A1W2PQC6, A0A1W2PQD8, A0A1W2PQJ5, A0A1W2PR75, A2AV36, A4QN59, A6QQV6, D4A1F2, F1RA39, G5E8F4, J9SQF3, O00142, O42868, O55239, O95050, O95932, O97972, P0CR76, P0CR77, P10938, P40261, P40936, P53538, Q01841, Q22453, Q32LP9, Q4R7D0, Q566Y1, Q5M9G7, Q5RFR7, Q5U4E8, Q5XG58, Q62160, Q6C195, Q6CQ61, Q6DE00, Q6FMU7, Q6PCI6

Diamond homologs: A0A1W2PQ27, A0A1W2PQ64, A0A1W2PQC6, A0A1W2PQD8, A0A1W2PQJ5, A0A1W2PR75, O42868, P0CR76, P0CR77, P53538, Q17QI2, Q22453, Q2HFZ9, Q2UPU5, Q4IPC8, Q4KLK9, Q4WHY5, Q558Z3, Q5ZJQ7, Q6BYP7, Q6C195, Q6CQ61, Q6FMU7, Q6NRQ7, Q6PC19, Q75E60, Q7SFY0, Q9CY97, Q9NP77

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1289 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:4329970:T:C	F36L	0.977
11:4329972:T:A	F36L	0.977
11:4329972:T:G	F36L	0.977
11:4330177:T:C	F105L	0.960
11:4330179:T:A	F105L	0.960
11:4330179:T:G	F105L	0.960
11:4330140:G:C	K92N	0.958
11:4330140:G:T	K92N	0.958
11:4330033:T:C	F57L	0.947
11:4330035:T:A	F57L	0.947
11:4330035:T:G	F57L	0.947
11:4330441:T:C	F193L	0.947
11:4330443:C:A	F193L	0.947
11:4330443:C:G	F193L	0.947
11:4330156:T:C	F98L	0.941
11:4330158:T:A	F98L	0.941
11:4330158:T:G	F98L	0.941
11:4330157:T:C	F98S	0.923
11:4329919:A:C	S19R	0.922
11:4329921:C:A	S19R	0.922
11:4329921:C:G	S19R	0.922
11:4330271:T:A	V136E	0.913
11:4330184:T:A	V107D	0.893
11:4330306:G:C	A148P	0.890
11:4330138:A:G	K92E	0.889
11:4330157:T:G	F98C	0.888
11:4330125:A:C	R87S	0.886
11:4330125:A:T	R87S	0.886
11:4330190:T:C	F109S	0.885
11:4330265:T:A	V134E	0.884

Disease associations

OMIM: gene `` | 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)

Clinical trials (associated diseases)

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