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Atlas / Gene / TSPY9

TSPY9

gene
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Summary

TSPY9 (testis specific protein Y-linked 9, HGNC:37472) is a protein-coding gene on chromosome Yp11.2, encoding Testis-specific Y-encoded protein 9 (A0A494C1R9). May be involved in sperm differentiation and proliferation.

Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in several processes, including gonadal mesoderm development; nucleosome assembly; and spermatogenesis. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleus.

Source: NCBI Gene 728132 — RefSeq curated summary.

At a glance

  • MANE Select transcript: NM_001396063

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:37472
Approved symbolTSPY9
Nametestis specific protein Y-linked 9
LocationYp11.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000238074
Ensembl biotypeprotein_coding
Entrez728132

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000440215

RefSeq mRNA: 1 — MANE Select: NM_001396063 NM_001396063

CCDS: CCDS94712

Canonical transcript exons

ENST00000440215 — 6 exons

ExonStartEnd
ENSE0000166381394884249488501
ENSE0000348264094890959489176
ENSE0000356998394886309488741
ENSE0000362210494888439488988
ENSE0000397825494872679487816
ENSE0000397825594898719490081

Expression profiles

Bgee: expression breadth tissue_specific, 9 present calls, max score 86.01.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.01gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.68gold quality
right testisUBERON:000453478.51gold quality
testisUBERON:000047376.00gold quality
left testisUBERON:000453375.55gold quality
colonic epitheliumUBERON:000039737.20gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
bone marrow cellCL:000209236.16gold quality
ganglionic eminenceUBERON:000402335.49gold quality
skeletal muscle tissueUBERON:000113433.38gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
bone marrowUBERON:000237131.74gold quality
muscle tissueUBERON:000238531.06gold quality
sural nerveUBERON:001548830.93gold quality
stromal cell of endometriumCL:000225529.87gold quality
prefrontal cortexUBERON:000045129.23gold quality
liverUBERON:000210728.32gold quality
duodenumUBERON:000211428.14gold quality
lymph nodeUBERON:000002927.57gold quality
tonsilUBERON:000237227.05gold quality
islet of LangerhansUBERON:000000626.55gold quality
vermiform appendixUBERON:000115426.42gold quality
leukocyteCL:000073826.27gold quality
monocyteCL:000057626.14gold quality
gall bladderUBERON:000211025.98gold quality
olfactory segment of nasal mucosaUBERON:000538625.89gold quality
bloodUBERON:000017825.88gold quality
placentaUBERON:000198725.81gold quality
muscle of legUBERON:000138324.87gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriotspyENSDARG00000005015
danio_rerionap1l4aENSDARG00000070560
drosophila_melanogasterSetFBGN0014879
drosophila_melanogasterNap1FBGN0015268
drosophila_melanogasterCG3708FBGN0040345
drosophila_melanogastermilFBGN0267366
caenorhabditis_elegansWBGENE00005007
caenorhabditis_elegansWBGENE00017075

Paralogs (19): SET (ENSG00000119335), TSPY2 (ENSG00000168757), NAP1L5 (ENSG00000177432), TSPYL6 (ENSG00000178021), TSPYL5 (ENSG00000180543), TSPYL2 (ENSG00000184205), NAP1L3 (ENSG00000186310), NAP1L2 (ENSG00000186462), NAP1L1 (ENSG00000187109), TSPYL4 (ENSG00000187189), TSPYL1 (ENSG00000189241), NAP1L4 (ENSG00000205531), TSPY3 (ENSG00000228927), TSPY8 (ENSG00000229549), SETSIP (ENSG00000230667), TSPY4 (ENSG00000233803), TSPY10 (ENSG00000236424), TSPY1 (ENSG00000258992), (ENSG00000293164)

Protein

Protein identifiers

Testis-specific Y-encoded protein 9 — A0A494C1R9 (reviewed: A0A494C1R9)

All UniProt accessions (1): A0A494C1R9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in sperm differentiation and proliferation.

Subcellular location. Cytoplasm. Nucleus.

Polymorphism. Maps to a tandemly repeated region on chromosome Yp11; additionally at least one copy is reported originating from Yq. The gene is thought to be present with an inter-individual variation in copy number and between 20 and 60 copies per Y chromosome are expected. 35 tandemly repeated gene copies on Yp11 originating from one individual have been reported.

Similarity. Belongs to the nucleosome assembly protein (NAP) family.

RefSeq proteins (1): NP_001382992* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002164NAPFamily
IPR037231NAP-like_sfHomologous_superfamily

Pfam: PF00956

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A0A494C1R9-F173.390.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, GOBP_SEX_DIFFERENTIATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MESENCHYME_DEVELOPMENT, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_MESODERM_DEVELOPMENT, GOBP_CHROMATIN_REMODELING, GOBP_DEVELOPMENT_OF_PRIMARY_SEXUAL_CHARACTERISTICS, GOMF_CHROMATIN_BINDING, GOMF_HISTONE_BINDING, chrYp11, GOBP_GONADAL_MESODERM_DEVELOPMENT, GOBP_NUCLEOSOME_ORGANIZATION, GOBP_SEXUAL_REPRODUCTION

GO Biological Process (4): nucleosome assembly (GO:0006334), spermatogenesis (GO:0007283), gonadal mesoderm development (GO:0007506), cell differentiation (GO:0030154)

GO Molecular Function (2): chromatin binding (GO:0003682), histone binding (GO:0042393)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
developmental process involved in reproduction2
cellular anatomical structure2
chromatin organization1
nucleosome organization1
protein-DNA complex assembly1
male gamete generation1
mesoderm development1
gonad development1
mesenchyme development1
cellular developmental process1
binding1
protein binding1
chromosome1
intracellular membrane-bounded organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: A0A494C1R9, A2ZX50, A6NKD2, B8AEC1, B8B2R4, B8B4K9, B9FU45, F4JEI8, O19110, O59797, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0DME0, P53997, P78920, Q01105, Q01534, Q0P5N2, Q18240, Q5R5G8, Q5VND6, Q63945, Q69JW2, Q69ZB3, Q70Z17, Q70Z18, Q70Z19, Q7TQI8, Q86VY4, Q8N831, Q8VD63, Q94K07, Q9BE64, Q9CA59, Q9EQU5, Q9H0U9, Q9H2G4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1083 predictions. Top by Δscore:

VariantEffectΔscore
Y:9488500:AGG:Adonor_loss1.0000
Y:9488501:GGTG:Gdonor_loss1.0000
Y:9488502:G:Tdonor_loss1.0000
Y:9488512:G:GTdonor_gain1.0000
Y:9488619:T:TAacceptor_gain1.0000
Y:9488624:T:Aacceptor_gain1.0000
Y:9488626:ACAG:Aacceptor_loss1.0000
Y:9488628:A:AGacceptor_gain1.0000
Y:9488628:AG:Aacceptor_gain1.0000
Y:9488628:AGGT:Aacceptor_gain1.0000
Y:9488628:AGGTG:Aacceptor_gain1.0000
Y:9488629:G:GCacceptor_gain1.0000
Y:9488629:GG:Gacceptor_gain1.0000
Y:9488629:GGT:Gacceptor_gain1.0000
Y:9488629:GGTG:Gacceptor_gain1.0000
Y:9488629:GGTGG:Gacceptor_gain1.0000
Y:9488708:G:GGdonor_gain1.0000
Y:9488720:G:GTdonor_gain1.0000
Y:9488841:A:AGacceptor_gain1.0000
Y:9488842:G:GGacceptor_gain1.0000
Y:9488842:GA:Gacceptor_gain1.0000
Y:9488842:GAAT:Gacceptor_gain1.0000
Y:9488842:GAATA:Gacceptor_gain1.0000
Y:9488868:A:AGacceptor_gain1.0000
Y:9488986:GAG:Gdonor_gain1.0000
Y:9488987:AGG:Adonor_loss1.0000
Y:9488989:G:GGdonor_gain1.0000
Y:9488989:GTGA:Gdonor_loss1.0000
Y:9488990:T:Gdonor_loss1.0000
Y:9487711:G:GTdonor_gain0.9900

AlphaMissense

2063 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
Y:9488719:G:CK224N0.999
Y:9488719:G:TK224N0.999
Y:9487802:T:CF164L0.995
Y:9487804:C:AF164L0.995
Y:9487804:C:GF164L0.995
Y:9488697:T:CF217S0.994
Y:9488944:T:AW266R0.994
Y:9488944:T:CW266R0.994
Y:9488678:T:CF211L0.993
Y:9488680:T:AF211L0.993
Y:9488680:T:GF211L0.993
Y:9488875:T:AW243R0.993
Y:9488875:T:CW243R0.993
Y:9488723:T:CY226H0.992
Y:9487803:T:CF164S0.990
Y:9488723:T:GY226D0.990
Y:9488724:A:CY226S0.990
Y:9488696:T:CF217L0.989
Y:9488698:C:AF217L0.989
Y:9488698:C:GF217L0.989
Y:9488717:A:GK224E0.989
Y:9488984:C:AA279D0.989
Y:9488466:G:CD183H0.987
Y:9488877:G:CW243C0.987
Y:9488877:G:TW243C0.987
Y:9488946:G:CW266C0.987
Y:9488946:G:TW266C0.987
Y:9488434:A:GH172R0.986
Y:9488948:T:CF267S0.986
Y:9487805:T:AW165R0.984

dbSNP variants (sampled 112 via entrez): RS1187529841 (Y:9489024 A>G), RS1194474203 (Y:9487762 G>C), RS1201136942 (Y:9490123 TTGTGTG>T,TTGTG,TTGTGTGTG), RS1211557239 (Y:9488550 G>C), RS1223087928 (Y:9487831 G>A), RS1231183059 (Y:9490492 T>A), RS1259002950 (Y:9487447 A>G), RS1276064905 (Y:9487226 C>T), RS1284855480 (Y:9488194 GTC>G), RS1317472486 (Y:9487656 T>C), RS1323524936 (Y:9485444 G>C), RS1331033658 (Y:9488535 G>C), RS1348459055 (Y:9487589 C>T), RS1369759669 (Y:9485494 C>T), RS1441031320 (Y:9485671 G>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)

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