CIMAP1A

Summary

CIMAP1A (ciliary microtubule associated protein 1A, HGNC:19905) is a protein-coding gene on chromosome 11p15.5, encoding Ciliary microtubule associated protein 1A (Q96PU9). Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail.

ODF3 is a component of sperm flagella outer dense fibers, which add stiffness, elastic recoil, and protection against shearing forces during sperm movement.

Source: NCBI Gene 113746 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_053280

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19905
Approved symbol	CIMAP1A
Name	ciliary microtubule associated protein 1A
Location	11p15.5
Locus type	gene with protein product
Status	Approved
Aliases	SHIPPO1, hSHIPPO, CT135
Ensembl gene	ENSG00000177947
Ensembl biotype	protein_coding
OMIM	608356
Entrez	113746

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000325113, ENST00000525282, ENST00000531679

RefSeq mRNA: 2 — MANE Select: NM_053280 NM_001286136, NM_053280

CCDS: CCDS65981, CCDS7688

Canonical transcript exons

ENST00000325113 — 7 exons

Exon	Start	End
ENSE00001267100	199369	199509
ENSE00001267106	198464	198585
ENSE00001267114	198199	198300
ENSE00001267138	196761	197046
ENSE00001365436	199944	200258
ENSE00001371629	197297	197413
ENSE00003620969	197561	197761

Expression profiles

Bgee: expression breadth broad, 28 present calls, max score 90.67.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	90.67	gold quality
kidney epithelium	UBERON:0004819	88.21	gold quality
epithelial cell of pancreas	CL:0000083	87.83	gold quality
vena cava	UBERON:0004087	86.42	gold quality
cerebellar vermis	UBERON:0004720	82.83	gold quality
superficial temporal artery	UBERON:0001614	82.68	gold quality
pancreatic ductal cell	CL:0002079	81.41	silver quality
mucosa of paranasal sinus	UBERON:0005030	79.71	gold quality
cardia of stomach	UBERON:0001162	79.44	gold quality
ventral tegmental area	UBERON:0002691	78.93	gold quality
layer of synovial tissue	UBERON:0007616	78.78	silver quality
substantia nigra pars compacta	UBERON:0001965	78.71	gold quality
body of tongue	UBERON:0011876	78.25	gold quality
pharyngeal mucosa	UBERON:0000355	77.93	gold quality
lateral nuclear group of thalamus	UBERON:0002736	77.91	gold quality
pericardium	UBERON:0002407	77.74	gold quality
trachea	UBERON:0003126	77.68	gold quality
saphenous vein	UBERON:0007318	77.66	gold quality
nipple	UBERON:0002030	77.62	gold quality
pons	UBERON:0000988	77.53	gold quality
upper arm skin	UBERON:0004263	77.17	gold quality
pylorus	UBERON:0001166	76.79	gold quality
renal medulla	UBERON:0000362	76.48	gold quality
oocyte	CL:0000023	76.40	gold quality
synovial joint	UBERON:0002217	76.33	gold quality
sperm	CL:0000019	76.11	gold quality
nasal cavity epithelium	UBERON:0005384	75.89	gold quality
epithelium of nasopharynx	UBERON:0001951	75.74	gold quality
penis	UBERON:0000989	75.66	silver quality
ileal mucosa	UBERON:0000331	74.78	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting CIMAP1A, 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-4455	100.00	65.48	1587
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-581	98.39	67.42	835
HSA-MIR-3920	97.75	69.02	1168

Literature-anchored findings (GeneRIF, showing 2)

• cloning and sequence analysis of h-shippo 1 an orthologue of mouse shippo 1 (PMID:11870087)
• Two alternative splice variants of ODF3 and ODF4, were found. (PMID:23096689)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimap1a	ENSMUSG00000025482
rattus_norvegicus	Cimap1a	ENSRNOG00000012858

Paralogs (5): STPG1 (ENSG00000001460), STPG2 (ENSG00000163116), CIMAP1B (ENSG00000177989), CIMAP1D (ENSG00000181781), CIMAP1C (ENSG00000182950)

Protein

Protein identifiers

Ciliary microtubule associated protein 1A — Q96PU9 (reviewed: Q96PU9)

Alternative names: Outer dense fiber of sperm tails protein 3, Outer dense fiber protein 3, Sperm tail protein SHIPPO 1, Transcript induced in spermiogenesis protein 50

All UniProt accessions (1): Q96PU9

UniProt curated annotations — full annotation on UniProt →

Function. Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic recoil of the sperm tail.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Tissue specificity. Testis-specific.

Miscellaneous. ‘Shippo’ is a Japanese word for tail.

Similarity. Belongs to the CIMAP family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96PU9-1	1	yes
Q96PU9-2	2
Q96PU9-3	3

RefSeq proteins (2): NP_001273065, NP_444510* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010736	SHIPPO-rpt	Repeat
IPR051291	CIMAP	Family

Pfam: PF07004

UniProt features (7 total): splice variant 3, repeat 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PU9-F1	74.04	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): SP3_Q3, GOBP_MALE_GAMETE_GENERATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_MOTILE_CILIUM, GOCC_CILIUM, GOCC_OUTER_DENSE_FIBER, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, MIR570_3P, GSE10240_IL22_VS_IL22_AND_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_DN, MIR29A_5P

GO Biological Process (3): spermatogenesis (GO:0007283), cell differentiation (GO:0030154), flagellated sperm motility (GO:0030317)

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

GO Cellular Component (7): outer dense fiber (GO:0001520), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), sperm flagellum (GO:0036126), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
binding	1
sperm flagellum	1
polymeric cytoskeletal fiber	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1
9+2 motile cilium	1

Protein interactions and networks

STRING

624 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMAP1A	ODF4	Q2M2E3	833
CIMAP1A	ODF1	Q14990	663
CIMAP1A	RIC8A	Q9NPQ8	616
CIMAP1A	SPATA19	Q7Z5L4	522
CIMAP1A	KIF3A	Q9Y496	520
CIMAP1A	ROPN1	Q9HAT0	486
CIMAP1A	ZPBP	Q9BS86	456
CIMAP1A	BET1	O15155	456
CIMAP1A	SPACA7	Q96KW9	456
CIMAP1A	SIRT3	Q9NTG7	451
CIMAP1A	SPAG8	Q99932	447
CIMAP1A	BET1L	Q9NYM9	446
CIMAP1A	TRHR	P34981	423
CIMAP1A	CABYR	O75952	422
CIMAP1A	AKAP3	O75969	421

IntAct

9 interactions, top by confidence:

A	B	Type	Score
DYNLL1	CIMAP1A	psi-mi:“MI:0915”(physical association)	0.560
HOGA1	CIMAP1A	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1A	HSPA8	psi-mi:“MI:0914”(association)	0.350
CIMAP1A	PKLR	psi-mi:“MI:0914”(association)	0.350
CIMAP1A	DYNLL1	psi-mi:“MI:0915”(physical association)	0.000
CIMAP1A	HOGA1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): ODF3 (Two-hybrid), HOGA1 (Two-hybrid), C12orf57 (Affinity Capture-MS), PSMG4 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), MMADHC (Affinity Capture-MS), ANKRD50 (Affinity Capture-MS), PKLR (Affinity Capture-MS), MED20 (Affinity Capture-MS), MED18 (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q1N1R0, A1A5R9, A2AVQ5, A3KGF7, A3KQA5, A4IH24, A5WUY6, B1H283, D4A1F2, E1BKH1, E7F9T0, F1RA39, O70209, O70400, O89040, P30944, P52944, P55292, Q00722, Q08BC4, Q2TBH0, Q2TBS4, Q32TF8, Q32TG3, Q3KQ80, Q3SX64, Q3SYZ8, Q3TZ65, Q4KLY8, Q4R7D3, Q5EB30, Q5JST6, Q5JVL4, Q5M8M2, Q6AYP6, Q6NUF4, Q810P2, Q8AVY1, Q8C8J0, Q8IXM7

Diamond homologs: A3KQA5, A8MYP8, Q2TBH0, Q3TZ65, Q5EB30, Q5M8M2, Q8AVY1, Q920N1, Q96PU9, Q3SX64, Q8IXM7, Q2KIH8, Q810P2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1251 predictions. Top by Δscore:

Variant	Effect	Δscore
11:197412:AGGT:A	donor_loss	1.0000
11:197413:GGTA:G	donor_loss	1.0000
11:197414:G:GA	donor_loss	1.0000
11:197414:G:GG	donor_gain	1.0000
11:199516:G:GT	donor_gain	1.0000
11:199517:A:T	donor_gain	1.0000
11:199527:C:G	donor_gain	1.0000
11:199531:GAGGG:G	donor_gain	1.0000
11:199533:GGG:G	donor_gain	1.0000
11:199534:GGG:G	donor_gain	1.0000
11:197410:ACAG:A	donor_gain	0.9900
11:197555:CCACA:C	acceptor_loss	0.9900
11:197556:CACA:C	acceptor_loss	0.9900
11:197559:A:AG	acceptor_gain	0.9900
11:197559:AG:A	acceptor_gain	0.9900
11:197559:AGG:A	acceptor_loss	0.9900
11:197560:G:GG	acceptor_gain	0.9900
11:197560:G:GT	acceptor_loss	0.9900
11:197560:GG:G	acceptor_gain	0.9900
11:197757:TCCAG:T	donor_loss	0.9900
11:197758:CCAG:C	donor_loss	0.9900
11:197760:AGG:A	donor_loss	0.9900
11:197761:GGT:G	donor_loss	0.9900
11:197762:G:C	donor_loss	0.9900
11:198462:A:AG	acceptor_gain	0.9900
11:198463:G:GG	acceptor_gain	0.9900
11:199368:GA:G	acceptor_gain	0.9900
11:199484:G:GT	donor_gain	0.9900
11:199507:A:T	donor_gain	0.9900
11:197411:CAG:C	donor_gain	0.9800

AlphaMissense

1644 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:197377:A:C	S25R	0.989
11:197379:C:A	S25R	0.989
11:197379:C:G	S25R	0.989
11:199376:G:A	G181D	0.989
11:197605:A:C	S52R	0.986
11:197607:C:A	S52R	0.986
11:197607:C:G	S52R	0.986
11:199484:G:A	G217E	0.986
11:197384:G:A	G27E	0.982
11:197651:G:A	G67E	0.982
11:198464:G:A	G138D	0.982
11:198300:G:C	G138R	0.981
11:197332:T:A	W10R	0.980
11:197332:T:C	W10R	0.980
11:199375:G:C	G181R	0.980
11:197650:G:T	G67W	0.978
11:197383:G:A	G27R	0.977
11:197383:G:C	G27R	0.977
11:197650:G:A	G67R	0.977
11:197650:G:C	G67R	0.977
11:197756:G:A	G102D	0.975
11:199483:G:A	G217R	0.975
11:199483:G:C	G217R	0.975
11:197392:T:C	Y30H	0.974
11:199492:G:C	A220P	0.974
11:197392:T:G	Y30D	0.972
11:197413:G:C	G37R	0.970
11:198565:T:C	F172L	0.970
11:198567:C:A	F172L	0.970
11:198567:C:G	F172L	0.970

dbSNP variants (sampled 300 via entrez): RS1000769170 (11:197112 C>A), RS1001975257 (11:196995 C>T), RS1002708698 (11:199739 G>A), RS1002949401 (11:196551 T>C), RS1003789229 (11:200706 G>C), RS1004395041 (11:198005 C>G), RS1004577779 (11:200336 G>C), RS1004593262 (11:200606 G>A), RS1005700100 (11:197750 C>T), RS1005871633 (11:195733 A>G), RS1006289364 (11:200499 T>C), RS1006675709 (11:199324 C>A,G,T), RS1007204198 (11:197472 C>T), RS1007290106 (11:199180 C>T), RS1007795426 (11:198611 G>A,C)

Disease associations

OMIM: gene MIM:608356 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST001027_3	Uterine fibroids	4.000000e-12
GCST002186_8	Platelet count	5.000000e-12
GCST004599_14	Mean platelet volume	7.000000e-163
GCST004603_55	Platelet count	4.000000e-103
GCST006001_12	Hemoglobin A1c levels	3.000000e-10
GCST007507_2	Benign prostatic hyperplasia and lower urinary tract symptoms	1.000000e-12
GCST007513_4	Prostate-specific antigen levels	6.000000e-06
GCST90002395_41	Mean platelet volume	6.000000e-41
GCST90002402_332	Platelet count	8.000000e-126
GCST90014268_24	Cataracts	4.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004309	platelet count
EFO:0004541	HbA1c measurement
EFO:0008008	lower urinary tract symptom

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation	1
testosterone undecanoate	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	decreases methylation	1
Valproic Acid	increases methylation	1
Levonorgestrel	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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