SECISBP2L

Summary

SECISBP2L (SECIS binding protein 2 like, HGNC:28997) is a protein-coding gene on chromosome 15q21.1, encoding Selenocysteine insertion sequence-binding protein 2-like (Q93073). Binds SECIS (Sec insertion sequence) elements present on selenocysteine (Sec) protein mRNAs, but does not promote Sec incorporation into selenoproteins in vitro.

Enables RNA binding activity. Predicted to be part of ribonucleoprotein complex. Predicted to be active in mitochondrion.

Source: NCBI Gene 9728 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 146 total
• MANE Select transcript: NM_001193489

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28997
Approved symbol	SECISBP2L
Name	SECIS binding protein 2 like
Location	15q21.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0256
Ensembl gene	ENSG00000138593
Ensembl biotype	protein_coding
OMIM	615756
Entrez	9728

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding, 5 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000261847, ENST00000380927, ENST00000557923, ENST00000557940, ENST00000558461, ENST00000559122, ENST00000559198, ENST00000559424, ENST00000559471, ENST00000561203, ENST00000561428, ENST00000910033, ENST00000910034

RefSeq mRNA: 2 — MANE Select: NM_001193489 NM_001193489, NM_014701

CCDS: CCDS32234, CCDS53942

Canonical transcript exons

ENST00000559471 — 18 exons

Exon	Start	End
ENSE00000931338	48996367	48996586
ENSE00000931340	49009216	49009378
ENSE00000931341	49011731	49011863
ENSE00000931342	49012648	49012817
ENSE00000931343	49016560	49016701
ENSE00000931344	49016848	49017015
ENSE00000942204	49035334	49035658
ENSE00000942207	49028144	49028168
ENSE00000942208	49027365	49027480
ENSE00000942209	49019418	49019552
ENSE00000942211	48999833	48999987
ENSE00001486847	48988638	48992926
ENSE00002556182	49046276	49046446
ENSE00003472368	49032965	49033100
ENSE00003509297	49028453	49028682
ENSE00003509747	49017548	49017628
ENSE00003517131	49037591	49037769
ENSE00003610852	49000877	49001097

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 99.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.8645 / max 1194.0314, expressed in 1821 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149808	41.5626	1813
149810	1.2420	583
149809	1.0333	598
149811	1.0265	219

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	99.38	gold quality
olfactory bulb	UBERON:0002264	99.29	gold quality
inferior vagus X ganglion	UBERON:0005363	99.22	gold quality
trigeminal ganglion	UBERON:0001675	99.19	gold quality
dorsal root ganglion	UBERON:0000044	99.04	gold quality
subthalamic nucleus	UBERON:0001906	98.94	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.43	gold quality
sural nerve	UBERON:0015488	98.40	gold quality
medulla oblongata	UBERON:0001896	98.38	gold quality
superior vestibular nucleus	UBERON:0007227	98.32	gold quality
ventral tegmental area	UBERON:0002691	98.28	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.18	gold quality
lateral globus pallidus	UBERON:0002476	98.15	gold quality
cranial nerve II	UBERON:0000941	98.02	gold quality
adrenal tissue	UBERON:0018303	98.02	gold quality
middle frontal gyrus	UBERON:0002702	97.95	gold quality
substantia nigra pars compacta	UBERON:0001965	97.80	gold quality
CA1 field of hippocampus	UBERON:0003881	97.73	gold quality
pons	UBERON:0000988	97.57	gold quality
calcaneal tendon	UBERON:0003701	97.37	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.02	gold quality
peripheral nervous system	UBERON:0000010	96.98	gold quality
tibial nerve	UBERON:0001323	96.98	gold quality
spinal cord	UBERON:0002240	96.81	gold quality
inferior olivary complex	UBERON:0002127	96.70	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.65	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.56	gold quality
orbitofrontal cortex	UBERON:0004167	96.38	gold quality
globus pallidus	UBERON:0001875	96.35	gold quality
endothelial cell	CL:0000115	96.19	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	22.36
E-GEOD-130148	yes	10.57
E-GEOD-111727	no	589.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

210 targeting SECISBP2L, 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-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593

Literature-anchored findings (GeneRIF, showing 3)

• SLAN, also known as KIAA0256. The novel protein suppressed in lung cancer down-regulated in lung cancer tissues retards cell proliferation and inhibits the oncokinase Aurora-A. (PMID:21566536)
• SECISBP2L (SBP2L) interacts with all known human SECIS RNAs in vitro and selenoprotein mRNAs co-immunoprecipitate with endogenous SBP2L, suggesting a role in regulating selenoprotein expression. (PMID:22530054)
• SLAN mediates the Aurora-A-triggered cytokinesis bypass and SLAN plays dual roles in that process depending on its phosphorylation status. (PMID:31314582)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000100084
mus_musculus	Secisbp2l	ENSMUSG00000035093
rattus_norvegicus	Secisbp2l	ENSRNOG00000008629
drosophila_melanogaster	Sbp2	FBGN0087039

Paralogs (1): SECISBP2 (ENSG00000187742)

Protein

Protein identifiers

Selenocysteine insertion sequence-binding protein 2-like — Q93073 (reviewed: Q93073)

All UniProt accessions (4): Q93073, H0YKY4, H0YNT4, J3KPI1

UniProt curated annotations — full annotation on UniProt →

Function. Binds SECIS (Sec insertion sequence) elements present on selenocysteine (Sec) protein mRNAs, but does not promote Sec incorporation into selenoproteins in vitro.

Isoforms (2)

UniProt ID	Names	Canonical?
Q93073-1	1	yes
Q93073-2	2

RefSeq proteins (2): NP_001180418, NP_055516 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004038	Ribosomal_eL8/eL30/eS12/Gad45	Domain
IPR029064	Ribosomal_eL30-like_sf	Homologous_superfamily
IPR040051	SECISBP2	Family

Pfam: PF01248

UniProt features (21 total): compositionally biased region 11, region of interest 5, chain 1, modified residue 1, splice variant 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q93073-F1	53.27	0.16

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 (1): 276

Mutagenesis-validated functional residues (1):

Position	Phenotype
721	loss of binding to selv and txnrd1 secis elements.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (1): selenocysteine incorporation (GO:0001514)

GO Molecular Function (5): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), selenocysteine insertion sequence binding (GO:0035368), ribonucleoprotein complex binding (GO:0043021), protein binding (GO:0005515)

GO Cellular Component (2): mitochondrion (GO:0005739), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mRNA binding	2
translational readthrough	1
nucleic acid binding	1
protein-containing complex binding	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

1888 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SECISBP2L	NSL1	Q96IY1	680
SECISBP2L	CD1C	P29017	508
SECISBP2L	EEFSEC	P57772	507
SECISBP2L	FCGR3A	P08637	506
SECISBP2L	FCGR3B	O75015	505
SECISBP2L	THBD	P07204	437
SECISBP2L	SELPLG	Q14242	436
SECISBP2L	PSTK	Q8IV42	431
SECISBP2L	CLEC4C	Q8WTT0	417
SECISBP2L	SELENOT	P62341	399
SECISBP2L	ITGAX	P20702	368
SECISBP2L	IL3RA	P26951	367
SECISBP2L	DTWD1	Q8N5C7	363
SECISBP2L	TLR7	Q9NYK1	326
SECISBP2L	CD163	Q86VB7	320

IntAct

26 interactions, top by confidence:

A	B	Type	Score
SECISBP2L	DYNLL2	psi-mi:“MI:0915”(physical association)	0.740
DYNLL2	SECISBP2L	psi-mi:“MI:0915”(physical association)	0.740
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
PSG9	CCDC85C	psi-mi:“MI:0914”(association)	0.530
INSYN2A	CHUK	psi-mi:“MI:0914”(association)	0.530
ZAR1L	BCL2L11	psi-mi:“MI:0914”(association)	0.530
ZYX	TBC1D10B	psi-mi:“MI:0914”(association)	0.530
RMND5A	DDX5	psi-mi:“MI:0914”(association)	0.510
SECISBP2L	RAN	psi-mi:“MI:0915”(physical association)	0.400
SECISBP2L	iglC2	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
CAMK2A	SMCHD1	psi-mi:“MI:0914”(association)	0.350
IQUB	GEMIN2	psi-mi:“MI:0914”(association)	0.350
ZYX	AAK1	psi-mi:“MI:0914”(association)	0.350
SF3B4	MED19	psi-mi:“MI:2364”(proximity)	0.270
DDX6	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
SECISBP2L	RMND5A	psi-mi:“MI:0915”(physical association)	0.000
rne	SECISBP2L	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (58): DYNLL2 (Two-hybrid), SECISBP2L (Affinity Capture-MS), SECISBP2L (Affinity Capture-MS), SECISBP2L (Affinity Capture-MS), SECISBP2L (Synthetic Lethality), SECISBP2L (Synthetic Lethality), SECISBP2L (Affinity Capture-MS), SECISBP2L (Affinity Capture-MS), SECISBP2L (Affinity Capture-MS), RMND5A (Affinity Capture-MS), SECISBP2L (Affinity Capture-RNA), SECISBP2L (Affinity Capture-MS), SECISBP2L (Two-hybrid), SECISBP2L (Proximity Label-MS), SECISBP2L (Proximity Label-MS)

ESM2 similar proteins: A0A1L8GR68, A2CG63, E9Q9M8, F7AQ22, G3V8T1, O75152, O75376, P49140, P51826, P97432, Q13625, Q14596, Q17R98, Q1LY51, Q3TYA6, Q4KKX4, Q4LE39, Q4R6F6, Q501R9, Q505G8, Q5F3Z9, Q5HYC2, Q5RC94, Q5XJV7, Q60974, Q68FE8, Q69Z61, Q6A098, Q6NXK2, Q6NZF1, Q6PJT7, Q6ZNC4, Q86YI8, Q8BFU3, Q8BJ05, Q8CCH7, Q8CG79, Q8CHY6, Q8K2W6, Q8ND24

Diamond homologs: Q3U1C4, Q6A098, Q93073, Q96T21, Q9QX72

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
AURKA	“up-regulates quantity”	SECISBP2L	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	119
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2631 predictions. Top by Δscore:

Variant	Effect	Δscore
15:48996362:CTTA:C	donor_loss	1.0000
15:48996363:TTA:T	donor_loss	1.0000
15:48996364:TA:T	donor_loss	1.0000
15:48996365:A:AC	donor_gain	1.0000
15:48996365:A:C	donor_loss	1.0000
15:48996365:AC:A	donor_gain	1.0000
15:48996366:C:CC	donor_gain	1.0000
15:48996366:CC:C	donor_gain	1.0000
15:48996366:CCATA:C	donor_gain	1.0000
15:48996582:AGGCT:A	acceptor_gain	1.0000
15:48996583:GGCT:G	acceptor_gain	1.0000
15:48996585:CT:C	acceptor_gain	1.0000
15:48996587:C:CC	acceptor_gain	1.0000
15:48996587:CT:C	acceptor_loss	1.0000
15:48996588:T:A	acceptor_loss	1.0000
15:48999827:TCTTA:T	donor_loss	1.0000
15:48999828:CTTA:C	donor_loss	1.0000
15:48999829:TTACC:T	donor_loss	1.0000
15:48999830:TACC:T	donor_loss	1.0000
15:48999831:ACCTC:A	donor_loss	1.0000
15:48999832:C:CG	donor_loss	1.0000
15:48999832:CCT:C	donor_gain	1.0000
15:48999984:CCAC:C	acceptor_gain	1.0000
15:48999985:CACC:C	acceptor_gain	1.0000
15:48999987:CCTG:C	acceptor_loss	1.0000
15:49000873:ATAC:A	donor_loss	1.0000
15:49000874:TACC:T	donor_loss	1.0000
15:49000875:ACCT:A	donor_loss	1.0000
15:49000876:C:CG	donor_loss	1.0000
15:49009214:A:AC	donor_gain	1.0000

AlphaMissense

7277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:48996538:A:C	Y818D	1.000
15:48999858:C:T	G793E	1.000
15:48999859:C:G	G793R	1.000
15:48999859:C:T	G793R	1.000
15:48999861:A:T	V792E	1.000
15:48999866:G:C	S790R	1.000
15:48999866:G:T	S790R	1.000
15:48999868:T:G	S790R	1.000
15:48999870:A:T	V789D	1.000
15:48999876:A:T	V787D	1.000
15:48999881:C:A	K785N	1.000
15:48999881:C:G	K785N	1.000
15:48999883:T:C	K785E	1.000
15:48999894:C:G	R781P	1.000
15:48999897:C:A	G780V	1.000
15:48999897:C:T	G780E	1.000
15:48999898:C:G	G780R	1.000
15:48999898:C:T	G780R	1.000
15:48999900:A:G	L779P	1.000
15:48999908:C:A	R776S	1.000
15:48999908:C:G	R776S	1.000
15:48999909:C:A	R776M	1.000
15:48999909:C:G	R776T	1.000
15:48999918:G:T	A773D	1.000
15:48999920:A:C	F772L	1.000
15:48999920:A:T	F772L	1.000
15:48999921:A:G	F772S	1.000
15:48999922:A:G	F772L	1.000
15:48999949:C:G	A763P	1.000
15:48999960:A:T	V759D	1.000

dbSNP variants (sampled 300 via entrez): RS1000083169 (15:49000806 C>A,T), RS1000096902 (15:49004253 G>C), RS1000112441 (15:49045869 T>C), RS1000122052 (15:49009400 G>A,T), RS1000177063 (15:49034743 C>T), RS1000261624 (15:49003783 T>G), RS1000349230 (15:49040872 A>G), RS1000357394 (15:49028052 T>A,C), RS1000358541 (15:48990903 A>C), RS1000459330 (15:48991846 C>A), RS1000510630 (15:49046520 G>A,C), RS1000614883 (15:48989635 T>C), RS1000668239 (15:49042707 T>G), RS1000688321 (15:49028264 G>A,T), RS1000690915 (15:49029558 G>A)

Disease associations

OMIM: gene MIM:615756 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST004744_31	Lung adenocarcinoma	2.000000e-16
GCST004748_33	Lung cancer	1.000000e-09
GCST004749_38	Lung cancer in ever smokers	2.000000e-07
GCST007328_57	Alcohol consumption (drinks per week)	4.000000e-08
GCST008152_107	Weight	4.000000e-06
GCST008836_8	Lung adenocarcinoma	7.000000e-12
GCST010204_66	Low density lipoprotein cholesterol levels	3.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004338	body weight
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, increases expression	2
sodium arsenite	decreases expression, increases expression	2
bisphenol F	affects cotreatment, increases expression	1
beta-N-methylamino-L-alanine	increases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
beta-lapachone	decreases expression, increases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Decitabine	affects expression	1
Zoledronic Acid	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Vorinostat	decreases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	affects expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Endosulfan	decreases expression	1
Formaldehyde	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Mustard Gas	increases expression	1
Plant Oils	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TK50	HAP1 SECISBP2L (-) 1	Cancer cell line	Male
CVCL_TK51	HAP1 SECISBP2L (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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