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Atlas / Gene / SPMIP5

SPMIP5

gene
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Also known as MGC33547Em:AC016825.4

Summary

SPMIP5 (sperm microtubule inner protein 5, HGNC:28500) is a protein-coding gene on chromosome 10q25.3, encoding Sperm-associated microtubule inner protein 5 (Q8WW14). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme.

Predicted to be involved in flagellated sperm motility. Predicted to be located in several cellular components, including cytoskeleton; motile cilium; and nucleus. Predicted to be active in axonemal A tubule inner sheath and sperm flagellum.

Source: NCBI Gene 143379 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 3 total
  • MANE Select transcript: NM_001350931

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28500
Approved symbolSPMIP5
Namesperm microtubule inner protein 5
Location10q25.3
Locus typegene with protein product
StatusApproved
AliasesMGC33547, Em:AC016825.4
Ensembl geneENSG00000165863
Ensembl biotypeprotein_coding
Entrez143379

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000369210, ENST00000467153, ENST00000588184, ENST00000588224, ENST00000865230, ENST00000865231, ENST00000936567, ENST00000936568, ENST00000936569

RefSeq mRNA: 4 — MANE Select: NM_001350931 NM_001330142, NM_001350930, NM_001350931, NM_144661

CCDS: CCDS7596, CCDS81510

Canonical transcript exons

ENST00000588184 — 6 exons

ExonStartEnd
ENSE00001193252116664761116664947
ENSE00001224087116665608116665826
ENSE00002898275116669927116669966
ENSE00002946554116663696116664051
ENSE00003469188116664174116664271
ENSE00003525384116668258116668323

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 97.92.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9490 / max 96.5322, expressed in 444 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1115591.7798438
1115550.07543
1115580.072741
1115570.01433
1115560.00693

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001997.92gold quality
left testisUBERON:000453395.62gold quality
right testisUBERON:000453495.02gold quality
secondary oocyteCL:000065594.61gold quality
testisUBERON:000047393.80gold quality
adult organismUBERON:000702393.53gold quality
oocyteCL:000002393.23gold quality
adrenal tissueUBERON:001830389.12gold quality
tibial nerveUBERON:000132384.57gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047377.78gold quality
epithelial cell of pancreasCL:000008377.57gold quality
cortical plateUBERON:000534375.96gold quality
cardiac muscle of right atriumUBERON:000337975.28gold quality
left ventricle myocardiumUBERON:000656675.21gold quality
mucosa of paranasal sinusUBERON:000503074.03gold quality
hypothalamusUBERON:000189873.63gold quality
left ovaryUBERON:000211971.24gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099170.24gold quality
ovaryUBERON:000099269.74gold quality
superficial temporal arteryUBERON:000161469.63gold quality
left lobe of thyroid glandUBERON:000112069.31gold quality
adrenal glandUBERON:000236968.42gold quality
right adrenal glandUBERON:000123368.25gold quality
thyroid glandUBERON:000204668.16gold quality
left adrenal glandUBERON:000123467.65gold quality
right lobe of thyroid glandUBERON:000111967.58gold quality
lower esophagus muscularis layerUBERON:003583367.42gold quality
lower esophagusUBERON:001347367.36gold quality
right adrenal gland cortexUBERON:003582767.22gold quality
right ovaryUBERON:000211867.21gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.42
E-MTAB-6379no2.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting SPMIP5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4533100.0069.482758
HSA-MIR-3156-3P99.7666.72939
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-324-3P99.2666.311034
HSA-MIR-4758-3P99.1263.96869
HSA-MIR-1178-3P98.5767.09890
HSA-MIR-4691-3P98.1166.831204
HSA-MIR-473697.9665.891287
HSA-MIR-428697.2064.371587
HSA-MIR-1306-5P97.1164.04755
HSA-MIR-6729-3P96.9166.79703
HSA-MIR-6820-5P94.0461.13161
HSA-MIR-55394.0165.93158
HSA-MIR-65888.2067.03178
HSA-MIR-1268A87.0661.46145
HSA-MIR-1268B87.0661.46145

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSpmip5ENSMUSG00000026931
rattus_norvegicusSpmip5ENSRNOG00000025953

Protein

Protein identifiers

Sperm-associated microtubule inner protein 5 — Q8WW14 (reviewed: Q8WW14)

All UniProt accessions (1): Q8WW14

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme. May serve to reinforce and thus stabilize the microtubule structure in the sperm flagella.

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

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme. Nucleus.

Tissue specificity. Expressed in testis (at protein level). Strongly expressed in peritubular cells and Leydig cells and weakly expressed in the cytoplasm of spermatocytes.

Isoforms (3)

UniProt IDNamesCanonical?
Q8WW14-11yes
Q8WW14-22
Q8WW14-33

RefSeq proteins (4): NP_001317071, NP_001337859, NP_001337860, NP_653262 (=MANE)

Domains & families (InterPro)

IDNameType
IPR043246SPMIP5Family
IPR055215SPMIP5_domDomain

Pfam: PF22573

UniProt features (5 total): splice variant 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WW14-F163.170.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, NKX25_02, PATIL_LIVER_CANCER, ATF1_Q6, NF1_Q6_01, AFP1_Q6, TGGNNNNNNKCCAR_UNKNOWN, chr10q25, HEB_Q6, FIGUEROA_AML_METHYLATION_CLUSTER_5_DN, FIGUEROA_AML_METHYLATION_CLUSTER_6_DN, FIGUEROA_AML_METHYLATION_CLUSTER_7_DN, IRF1_01, ESC_J1_UP_EARLY.V1_UP, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP

GO Biological Process (0):

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

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
intracellular membraneless organelle1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
cilium1

Protein interactions and networks

STRING

292 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPMIP5TMEM234Q8WY98418
SPMIP5RPP21Q9H633397
SPMIP5TCEAL8Q8IYN2371
SPMIP5RNF17Q9BXT8367
SPMIP5MAGEB6Q8N7X4359
SPMIP5UBE2UQ5VVX9350
SPMIP5SPATA22Q8NHS9343
SPMIP5FOXR1Q6PIV2342
SPMIP5ASIC5Q9NY37341
SPMIP5LRRC52Q8N7C0337
SPMIP5AVL9Q8NBF6337
SPMIP5FABP12A6NFH5331
SPMIP5ZFYVE28Q9HCC9325
SPMIP5VWA7Q9Y334322
SPMIP5EQTNQ9NQ60321

IntAct

4 interactions, top by confidence:

ABTypeScore
RIMOC1SPMIP5psi-mi:“MI:0915”(physical association)0.400
TEX11SPMIP5psi-mi:“MI:0915”(physical association)0.370
SPMIP5WDHD1psi-mi:“MI:0914”(association)0.350

BioGRID (14): C10orf82 (Two-hybrid), C10orf82 (Two-hybrid), C10orf82 (Two-hybrid), C10orf82 (Two-hybrid), C10orf82 (Two-hybrid), ANKRD11 (Two-hybrid), MKRN3 (Two-hybrid), GPSM3 (Two-hybrid), WDHD1 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), CCDC51 (Affinity Capture-MS), TDP2 (Affinity Capture-MS), KIF3A (Affinity Capture-MS), C10orf82 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WRI3, A2BFC9, A2RRW4, A4QMS7, A6NJV1, A6NL82, A6QPC0, A6QQ68, A8E4X8, A8E5W8, A8QW39, A9JS51, D6REC4, F1P3Y5, G3X6E2, P0C875, Q0VB26, Q1MSJ5, Q2IA00, Q2T9Q3, Q2TA11, Q3UY96, Q494V2, Q497Q6, Q4KKZ1, Q4QR77, Q4R5Y0, Q4R8V8, Q5NC57, Q5ZIH9, Q6J272, Q6PII3, Q6ZQR2, Q6ZVS7, Q7Z4T9, Q8CFW7, Q8N1D5, Q8N6G2, Q8WW14, Q95LR0

Diamond homologs: A6QPC0, Q8WW14, Q9CQT6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance2
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

850 predictions. Top by Δscore:

VariantEffectΔscore
10:116664170:TCAC:Tdonor_loss1.0000
10:116664171:CACCT:Cdonor_loss1.0000
10:116664172:ACCTG:Adonor_loss1.0000
10:116664173:CCTG:Cdonor_loss1.0000
10:116664267:ATATT:Aacceptor_gain1.0000
10:116664268:TATT:Tacceptor_gain1.0000
10:116664269:ATT:Aacceptor_gain1.0000
10:116664270:TT:Tacceptor_gain1.0000
10:116664271:TCTA:Tacceptor_loss1.0000
10:116664272:C:CCacceptor_gain1.0000
10:116664278:C:CTacceptor_gain1.0000
10:116664279:A:Tacceptor_gain1.0000
10:116664755:ACT:Adonor_loss1.0000
10:116664756:CTC:Cdonor_loss1.0000
10:116664757:TCA:Tdonor_loss1.0000
10:116664759:A:ACdonor_gain1.0000
10:116664759:A:Cdonor_loss1.0000
10:116664759:ACT:Adonor_gain1.0000
10:116664760:C:CGdonor_gain1.0000
10:116664760:CT:Cdonor_gain1.0000
10:116664760:CTC:Cdonor_gain1.0000
10:116664760:CTCT:Cdonor_gain1.0000
10:116664760:CTCTT:Cdonor_gain1.0000
10:116665607:C:Adonor_gain1.0000
10:116665626:A:ACdonor_gain1.0000
10:116665627:C:CCdonor_gain1.0000
10:116665629:G:GAdonor_gain1.0000
10:116665638:A:ACdonor_gain1.0000
10:116665639:C:CCdonor_gain1.0000
10:116665664:T:TAdonor_gain1.0000

AlphaMissense

1522 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:116664900:A:GW108R0.988
10:116664900:A:TW108R0.988
10:116665822:A:CF20L0.981
10:116665822:A:TF20L0.981
10:116665824:A:GF20L0.981
10:116664898:C:AW108C0.977
10:116664898:C:GW108C0.977
10:116664811:G:CF137L0.972
10:116664811:G:TF137L0.972
10:116664813:A:GF137L0.972
10:116664823:G:CC133W0.970
10:116664825:A:GC133R0.969
10:116668292:G:CF7L0.964
10:116668292:G:TF7L0.964
10:116668294:A:GF7L0.964
10:116664880:T:AR114S0.960
10:116664880:T:GR114S0.960
10:116665756:G:CF42L0.955
10:116665756:G:TF42L0.955
10:116665758:A:GF42L0.955
10:116668286:T:AR9S0.952
10:116668286:T:GR9S0.952
10:116664899:C:GW108S0.949
10:116664834:C:GA130P0.948
10:116664884:G:TP113Q0.945
10:116664869:G:AT118I0.943
10:116664887:A:GL112P0.943
10:116668258:C:GG19R0.943
10:116664902:C:TG107D0.939
10:116665646:A:GL79P0.939

dbSNP variants (sampled 300 via entrez): RS1000145952 (10:116662262 G>C), RS1000990091 (10:116668106 C>A,T), RS1002321136 (10:116662761 A>C), RS1002344527 (10:116669216 A>T), RS1002374092 (10:116668914 C>A,G), RS1002643896 (10:116670603 A>G), RS1002711037 (10:116670287 G>A,C), RS1002784850 (10:116670135 G>A), RS1004045241 (10:116664702 T>C), RS1005349879 (10:116670720 C>T), RS1005687284 (10:116666248 C>T), RS1005718446 (10:116665956 T>C), RS1006030887 (10:116667599 C>A,T), RS1006060425 (10:116667336 G>A), RS1006581436 (10:116666641 C>T)

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

1 associations (top):

StudyTraitp-value
GCST005951_66Body mass index4.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sdecreases methylation1
Vorinostataffects cotreatment, decreases expression1
Leflunomideincreases expression1
Benzo(a)pyrenedecreases methylation1
Leadaffects expression1
Urethanedecreases expression1
Valproic Acidincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot