YJU2B

Summary

YJU2B (YJU2 splicing factor homolog B, HGNC:28118) is a protein-coding gene on chromosome 19p13.13, encoding Probable splicing factor YJU2B (P13994). May be involved in mRNA splicing. It is a selective cancer dependency (DepMap: 83.3% of cell lines).

Involved in response to virus. Predicted to be located in nucleus. Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex.

Source: NCBI Gene 81576 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 75 total
• Cancer dependency (DepMap): dependent in 83.3% of screened cell lines
• MANE Select transcript: NM_030818

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28118
Approved symbol	YJU2B
Name	YJU2 splicing factor homolog B
Location	19p13.13
Locus type	gene with protein product
Status	Approved
Aliases	MGC10471
Ensembl gene	ENSG00000104957
Ensembl biotype	protein_coding
Entrez	81576

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000221554, ENST00000540216, ENST00000585844, ENST00000586600, ENST00000586666, ENST00000587019, ENST00000587098, ENST00000588071, ENST00000588809, ENST00000589096, ENST00000589669, ENST00000593174, ENST00000865480, ENST00000865481, ENST00000865482, ENST00000865483, ENST00000865484, ENST00000938424

RefSeq mRNA: 8 — MANE Select: NM_030818 NM_001320561, NM_001320564, NM_001320565, NM_001320566, NM_001320567, NM_001320568, NM_001320569, NM_030818

CCDS: CCDS12296

Canonical transcript exons

ENST00000221554 — 10 exons

Exon	Start	End
ENSE00000684838	13759100	13759272
ENSE00000836478	13758868	13759010
ENSE00001763365	13762590	13763289
ENSE00002799491	13747895	13747954
ENSE00003462914	13751608	13751811
ENSE00003502195	13762299	13762437
ENSE00003516197	13754289	13754342
ENSE00003537540	13757418	13757473
ENSE00003637203	13756197	13756279
ENSE00003638897	13757786	13757846

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 97.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.6640 / max 156.6170, expressed in 1816 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174156	15.1742	1807
174152	5.8466	1694
174154	1.4966	952
174155	0.8032	533
208700	0.2125	82
174153	0.1309	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	97.05	gold quality
right lobe of thyroid gland	UBERON:0001119	96.66	gold quality
apex of heart	UBERON:0002098	96.22	gold quality
right ovary	UBERON:0002118	96.14	gold quality
left ovary	UBERON:0002119	96.13	gold quality
left lobe of thyroid gland	UBERON:0001120	96.05	gold quality
metanephros cortex	UBERON:0010533	95.87	gold quality
right uterine tube	UBERON:0001302	95.77	gold quality
left uterine tube	UBERON:0001303	95.70	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.66	gold quality
mucosa of stomach	UBERON:0001199	95.63	gold quality
adenohypophysis	UBERON:0002196	95.51	gold quality
nerve	UBERON:0001021	95.48	gold quality
tibial nerve	UBERON:0001323	95.48	gold quality
body of uterus	UBERON:0009853	95.46	gold quality
lower esophagus mucosa	UBERON:0035834	95.30	gold quality
endocervix	UBERON:0000458	95.19	gold quality
ectocervix	UBERON:0012249	95.05	gold quality
thyroid gland	UBERON:0002046	95.03	gold quality
transverse colon	UBERON:0001157	94.82	gold quality
body of stomach	UBERON:0001161	94.75	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.67	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.50	gold quality
skin of leg	UBERON:0001511	94.47	gold quality
minor salivary gland	UBERON:0001830	94.46	gold quality
spleen	UBERON:0002106	94.43	gold quality
mucosa of transverse colon	UBERON:0004991	94.41	gold quality
pituitary gland	UBERON:0000007	94.38	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.29	gold quality
skin of abdomen	UBERON:0001416	94.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.31
E-MTAB-6386	no	770.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting YJU2B, 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-6825-5P	99.96	69.81	3431
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-4733-3P	98.35	65.20	994

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 83.3% of screened cell lines.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yju2b	ENSDARG00000041533
mus_musculus	Yju2b	ENSMUSG00000004994
rattus_norvegicus	Yju2b	ENSRNOG00000008319
drosophila_melanogaster	CG15084	FBGN0034402
caenorhabditis_elegans		WBGENE00014250

Paralogs (1): YJU2 (ENSG00000105248)

Protein

Protein identifiers

Probable splicing factor YJU2B — P13994 (reviewed: P13994)

Alternative names: Coiled-coil domain-containing protein 130

All UniProt accessions (5): P13994, K7EJZ6, K7ELI4, K7EP29, K7ES43

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in mRNA splicing.

Subcellular location. Nucleus.

Induction. By poly(RI), poly(RC) and Newcastle disease virus.

Similarity. Belongs to the CWC16 family.

RefSeq proteins (8): NP_001307490, NP_001307493, NP_001307494, NP_001307495, NP_001307496, NP_001307497, NP_001307498, NP_110445* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007590	Saf4/Yju2	Family

Pfam: PF04502

UniProt features (11 total): modified residue 3, region of interest 2, sequence variant 2, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P13994-F1	73.24	0.33

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 (3): 40, 306, 362

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, CREBP1_Q2, CREB_Q4, GTGCCTT_MIR506, E4F1_Q6, GOBP_RNA_SPLICING, ATF4_Q2, GOBP_MRNA_CIS_SPLICING_VIA_SPLICEOSOME, GOBP_RESPONSE_TO_VIRUS, GOCC_U2_TYPE_SPLICEOSOMAL_COMPLEX, CGTSACG_PAX3_B, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, chr19p13, SCGGAAGY_ELK1_02

GO Biological Process (3): mRNA splicing, via spliceosome (GO:0000398), RNA splicing (GO:0008380), response to virus (GO:0009615)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): U2-type spliceosomal complex (GO:0005684), post-mRNA release spliceosomal complex (GO:0071014), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spliceosomal complex	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA processing	1
response to other organism	1
binding	1
U5 snRNP	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

670 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YJU2B	GPATCH11	Q8N954	580
YJU2B	C19orf67	A6NJJ6	542
YJU2B	RTF2	Q9BY42	499
YJU2B	NRDC	O43847	467
YJU2B	SNRPF	P62306	466
YJU2B	MRPL32	Q9BYC8	448
YJU2B	SMU1	Q2TAY7	447
YJU2B	PRR22	Q8IZ63	447
YJU2B	SDE2	Q6IQ49	446
YJU2B	PRKRIP1	Q9H875	437
YJU2B	CWC22	Q9HCG8	434
YJU2B	SPAG8	Q99932	428
YJU2B	TTC14	Q96N46	420
YJU2B	FN3KRP	Q9HA64	412
YJU2B	FATE1	Q969F0	406
YJU2B	C19orf53	Q9UNZ5	406

IntAct

95 interactions, top by confidence:

A	B	Type	Score
PRPF19	AQR	psi-mi:“MI:0914”(association)	0.790
ZNF165	YJU2B	psi-mi:“MI:0915”(physical association)	0.770
YJU2B	ZNF165	psi-mi:“MI:0915”(physical association)	0.770
ZNF24	YJU2B	psi-mi:“MI:0915”(physical association)	0.740
YJU2B	ZNF24	psi-mi:“MI:0915”(physical association)	0.740
YJU2B	ZNF572	psi-mi:“MI:0915”(physical association)	0.720
ZNF572	YJU2B	psi-mi:“MI:0915”(physical association)	0.720
ZNF629	YJU2B	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZFP3	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	TSSK3	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	CLP1	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZSCAN23	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF17	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	EFHC1	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	YJU2B	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF3	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	SMARCD1	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF250	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF629	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (83): ZNF572 (Two-hybrid), ZZEF1 (Affinity Capture-MS), UBR1 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), KDM8 (Affinity Capture-MS), SEPHS1 (Affinity Capture-MS), MINA (Affinity Capture-MS), CCDC130 (Two-hybrid), CCDC130 (Two-hybrid), CCDC130 (Two-hybrid), CCDC130 (Two-hybrid), CCDC130 (Affinity Capture-Western), KDM8 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS)

ESM2 similar proteins: A8WHR3, E7EXT2, G5EBY0, O15541, O60141, O74517, O94667, P13994, P28320, P28518, P28519, P34648, P35601, P38326, P53709, P78794, Q09651, Q0JHZ2, Q0VBD2, Q28C44, Q28E45, Q32PZ9, Q56P03, Q5EA37, Q5EAW4, Q5RHY1, Q5RJT2, Q66I85, Q67ER4, Q6C3L4, Q6DBR4, Q6DJK9, Q7K0F0, Q7L590, Q8BP78, Q8IQ05, Q8IY81, Q8N954, Q9BW85, Q9C950

Diamond homologs: A8WHR3, P13994, P28320, Q09651, Q32PZ9, Q54TR4, Q54WR5, Q5EA37, Q66I85, Q6DJK9, Q7K0F0, Q9BW85, Q9D516, Q9D6J3, Q9P7C5, O60141

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1451 predictions. Top by Δscore:

Variant	Effect	Δscore
19:13731825:G:GT	donor_gain	1.0000
19:13731841:GGGGC:G	donor_gain	1.0000
19:13731852:GGA:G	donor_gain	1.0000
19:13732283:GAG:G	donor_gain	1.0000
19:13732285:GGTGA:G	donor_loss	1.0000
19:13732286:G:C	donor_loss	1.0000
19:13754283:TTGCA:T	acceptor_loss	1.0000
19:13754286:CAGG:C	acceptor_loss	1.0000
19:13754287:A:AG	acceptor_gain	1.0000
19:13754287:AG:A	acceptor_gain	1.0000
19:13754287:AGG:A	acceptor_gain	1.0000
19:13754287:AGGGT:A	acceptor_gain	1.0000
19:13754288:G:A	acceptor_loss	1.0000
19:13754288:G:GA	acceptor_gain	1.0000
19:13754288:GG:G	acceptor_gain	1.0000
19:13754288:GGG:G	acceptor_gain	1.0000
19:13754288:GGGT:G	acceptor_gain	1.0000
19:13754288:GGGTG:G	acceptor_gain	1.0000
19:13754339:GAAG:G	donor_gain	1.0000
19:13754341:AGG:A	donor_loss	1.0000
19:13754343:G:GA	donor_loss	1.0000
19:13754343:G:GG	donor_gain	1.0000
19:13756191:A:AG	acceptor_gain	1.0000
19:13756192:C:G	acceptor_gain	1.0000
19:13756193:A:AG	acceptor_gain	1.0000
19:13756193:ACAGC:A	acceptor_loss	1.0000
19:13756194:C:G	acceptor_gain	1.0000
19:13756194:CAGCA:C	acceptor_loss	1.0000
19:13756195:A:AG	acceptor_gain	1.0000
19:13756195:AGCAT:A	acceptor_gain	1.0000

AlphaMissense

2615 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:13757419:T:C	F48L	1.000
19:13757421:C:A	F48L	1.000
19:13757421:C:G	F48L	1.000
19:13758869:T:C	F87L	1.000
19:13758870:T:C	F87S	1.000
19:13758871:C:A	F87L	1.000
19:13758871:C:G	F87L	1.000
19:13758881:T:C	C91R	1.000
19:13754328:T:C	F15L	0.999
19:13754330:C:A	F15L	0.999
19:13754330:C:G	F15L	0.999
19:13756278:C:G	R47G	0.999
19:13757420:T:C	F48S	0.999
19:13757424:A:C	E49D	0.999
19:13757424:A:T	E49D	0.999
19:13757426:T:G	M50R	0.999
19:13757429:C:A	P51Q	0.999
19:13757443:T:A	C56S	0.999
19:13757443:T:C	C56R	0.999
19:13757444:G:A	C56Y	0.999
19:13757444:G:C	C56S	0.999
19:13757444:G:T	C56F	0.999
19:13757452:T:A	C59S	0.999
19:13757453:G:C	C59S	0.999
19:13757473:G:C	G66R	0.999
19:13757786:G:A	G66D	0.999
19:13757791:C:A	R68S	0.999
19:13757794:T:C	Y69H	0.999
19:13757794:T:G	Y69D	0.999
19:13757799:T:A	N70K	0.999

dbSNP variants (sampled 300 via entrez): RS1000024796 (19:13751981 G>T), RS1000134359 (19:13757351 G>A,T), RS1000190133 (19:13757155 G>A), RS1000442169 (19:13739808 C>T), RS1000514000 (19:13746003 G>A,C), RS1000617737 (19:13736750 G>A), RS1000674948 (19:13750622 G>C), RS1000743726 (19:13762237 G>C), RS1000824265 (19:13730472 A>G), RS1000918239 (19:13747875 C>A,T), RS1000948298 (19:13745746 T>C,G), RS1000952251 (19:13760680 T>C), RS1000971787 (19:13747743 C>A,T), RS1001080879 (19:13752888 G>T), RS1001173195 (19:13730189 T>A)

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)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tunicamycin	increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
bisphenol A	decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases abundance, increases expression	1
resorcinol	decreases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	decreases expression	1
K 7174	increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Sunitinib	increases expression	1
Arsenic	increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Diazinon	increases methylation	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Theophylline	affects cotreatment, decreases expression	1
Urethane	increases expression	1
Zinc Sulfate	increases expression	1

Clinical trials (associated diseases)

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