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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 16654

FusionGeneSummary for HNRNPU_SLC36A4

check button Fusion gene summary
Fusion gene informationFusion gene name: HNRNPU_SLC36A4
Fusion gene ID: 16654
HgeneTgene
Gene symbol

HNRNPU

SLC36A4

Gene ID

3192

120103

Gene nameheterogeneous nuclear ribonucleoprotein Usolute carrier family 36 member 4
SynonymsEIEE54|GRIP120|HNRNPU-AS1|HNRPU|SAF-A|SAFA|U21.1|hnRNP U|pp120PAT4
Cytomap

1q44

11q21

Type of geneprotein-codingprotein-coding
Descriptionheterogeneous nuclear ribonucleoprotein UHNRNPU antisense RNA 1heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)nuclear p120 ribonucleoproteinp120 nuclear proteinproton-coupled amino acid transporter 4solute carrier family 36 (proton/amino acid symporter), member 4
Modification date2018051920180523
UniProtAcc

Q00839

Q6YBV0

Ensembl transtripts involved in fusion geneENST00000444376, ENST00000283179, 
ENST00000326402, ENST00000529184, 
Fusion gene scores* DoF score7 X 10 X 2=1401 X 1 X 1=1
# samples 121
** MAII scorelog2(12/140*10)=-0.222392421336448
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: HNRNPU [Title/Abstract] AND SLC36A4 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneHNRNPU

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

22325991

HgeneHNRNPU

GO:0048255

mRNA stabilization

17174306

HgeneHNRNPU

GO:0071385

cellular response to glucocorticoid stimulus

9353307

TgeneSLC36A4

GO:0015808

L-alanine transport

21097500

TgeneSLC36A4

GO:0015824

proline transport

21097500

TgeneSLC36A4

GO:0015827

tryptophan transport

21097500


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDPRADTCGA-KK-A8I8-01AHNRNPUchr1

245021313

-SLC36A4chr11

92918980

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000444376ENST00000326402HNRNPUchr1

245021313

-SLC36A4chr11

92918980

-
5CDS-5UTRENST00000444376ENST00000529184HNRNPUchr1

245021313

-SLC36A4chr11

92918980

-
Frame-shiftENST00000283179ENST00000326402HNRNPUchr1

245021313

-SLC36A4chr11

92918980

-
5CDS-5UTRENST00000283179ENST00000529184HNRNPUchr1

245021313

-SLC36A4chr11

92918980

-

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FusionProtFeatures for HNRNPU_SLC36A4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
HNRNPU

Q00839

SLC36A4

Q6YBV0

DNA- and RNA-binding protein involved in severalcellular processes such as nuclear chromatin organization,telomere-length regulation, transcription, mRNA alternativesplicing and stability, Xist-mediated transcriptional silencingand mitotic cell progression (PubMed:10490622, PubMed:18082603,PubMed:19029303, PubMed:22325991, PubMed:25986610,PubMed:28622508). Plays a role in the regulation of interphaselarge-scale gene-rich chromatin organization through chromatin-associated RNAs (caRNAs) in a transcription-dependent manner, andthereby maintains genomic stability (PubMed:1324173,PubMed:8174554, PubMed:28622508). Required for the localization ofthe long non-coding Xist RNA on the inactive chromosome X (Xi) andthe subsequent initiation and maintenance of X-linkedtranscriptional gene silencing during X-inactivation (Bysimilarity). Plays a role as a RNA polymerase II (Pol II)holoenzyme transcription regulator (PubMed:8174554,PubMed:9353307, PubMed:10490622, PubMed:15711563, PubMed:19617346,PubMed:23811339). Promotes transcription initiation by directassociation with the core-TFIIH basal transcription factor complexfor the assembly of a functional pre-initiation complex with PolII in a actin-dependent manner (PubMed:10490622, PubMed:15711563).Blocks Pol II transcription elongation activity by inhibiting theC-terminal domain (CTD) phosphorylation of Pol II and dissociatesfrom Pol II pre-initiation complex prior to productivetranscription elongation (PubMed:10490622). Positively regulatesCBX5-induced transcriptional gene silencing and retention of CBX5in the nucleus (PubMed:19617346). Negatively regulatesglucocorticoid-mediated transcriptional activation(PubMed:9353307). Key regulator of transcription initiation andelongation in embryonic stem cells upon leukemia inhibitory factor(LIF) signaling (By similarity). Involved in the long non-codingRNA H19-mediated Pol II transcriptional repression(PubMed:23811339). Participates in the circadian regulation of thecore clock component ARNTL/BMAL1 transcription (By similarity).Plays a role in the regulation of telomere length(PubMed:18082603). Plays a role as a global pre-mRNA alternativesplicing modulator by regulating U2 small nuclearribonucleoprotein (snRNP) biogenesis (PubMed:22325991). Plays arole in mRNA stability (PubMed:17174306, PubMed:17289661,PubMed:19029303). Component of the CRD-mediated complex thatpromotes MYC mRNA stabilization (PubMed:19029303). Enhances theexpression of specific genes, such as tumor necrosis factor TNFA,by regulating mRNA stability, possibly through binding to the 3'-untranslated region (UTR) (PubMed:17174306). Plays a role inmitotic cell cycle regulation (PubMed:21242313, PubMed:25986610).Involved in the formation of stable mitotic spindle microtubules(MTs) attachment to kinetochore, spindle organization andchromosome congression (PubMed:21242313). Phosphorylation at Ser-59 by PLK1 is required for chromosome alignement and segregationand progression through mitosis (PubMed:25986610). Contributesalso to the targeting of AURKA to mitotic spindle MTs(PubMed:21242313). Binds to double- and single-stranded DNA andRNA, poly(A), poly(C) and poly(G) oligoribonucleotides(PubMed:1628625, PubMed:8068679, PubMed:8174554, PubMed:9204873,PubMed:9405365). Binds to chromatin-associated RNAs (caRNAs)(PubMed:28622508). Associates with chromatin to scaffold/matrixattachment region (S/MAR) elements in a chromatin-associated RNAs(caRNAs)-dependent manner (PubMed:7509195, PubMed:1324173,PubMed:9204873, PubMed:9405365, PubMed:10671544, PubMed:11003645,PubMed:11909954, PubMed:28622508). Binds to the Xist RNA(PubMed:26244333). Binds the long non-coding H19 RNA(PubMed:23811339). Binds to SMN1/2 pre-mRNAs at G/U-rich regions(PubMed:22325991). Binds to small nuclear RNAs (snRNAs)(PubMed:22325991). Binds to the 3'-UTR of TNFA mRNA(PubMed:17174306). Binds (via RNA-binding RGG-box region) to thelong non-coding Xist RNA; this binding is direct and bridges theXist RNA and the inactive chromosome X (Xi) (By similarity). Alsonegatively regulates embryonic stem cell differentiation upon LIFsignaling (By similarity). Required for embryonic development (Bysimilarity). Binds to brown fat long non-coding RNA 1 (Blnc1);facilitates the recruitment of Blnc1 by ZBTB7B required to drivebrown and beige fat development and thermogenesis (By similarity).{ECO:0000250|UniProtKB:Q8VEK3, ECO:0000269|PubMed:10490622,ECO:0000269|PubMed:10671544, ECO:0000269|PubMed:11003645,ECO:0000269|PubMed:11909954, ECO:0000269|PubMed:1324173,ECO:0000269|PubMed:15711563, ECO:0000269|PubMed:1628625,ECO:0000269|PubMed:17174306, ECO:0000269|PubMed:17289661,ECO:0000269|PubMed:18082603, ECO:0000269|PubMed:19029303,ECO:0000269|PubMed:19617346, ECO:0000269|PubMed:21242313,ECO:0000269|PubMed:22325991, ECO:0000269|PubMed:23811339,ECO:0000269|PubMed:25986610, ECO:0000269|PubMed:26244333,ECO:0000269|PubMed:28622508, ECO:0000269|PubMed:7509195,ECO:0000269|PubMed:8068679, ECO:0000269|PubMed:8174554,ECO:0000269|PubMed:9204873, ECO:0000269|PubMed:9353307,ECO:0000269|PubMed:9405365}. (Microbial infection) Negatively regulatesimmunodeficiency virus type 1 (HIV-1) replication by preventingthe accumulation of viral mRNA transcripts in the cytoplasm.{ECO:0000269|PubMed:16916646}. Functions as a sodium-independent electroneutraltransporter for tryptophan, proline and alanine. Inhibited bysarcosine. {ECO:0000269|PubMed:21097500}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for HNRNPU_SLC36A4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for HNRNPU_SLC36A4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
HNRNPUSFN, EP300, PRMT1, NR3C1, GTF2F1, POLR2A, CDK7, NDN, GPN1, CDK9, RUVBL2, HNRNPH1, POLR2J, MYC, MAX, PML, RARA, EMD, MORF4L1, MORF4L2, MRGBP, DOT1L, NPM1, UBC, SNW1, DGCR8, RBM39, NOP56, DYRK2, STAU1, IKBKB, NFKBIA, BTRC, VHL, RNF146, SMARCAD1, SREK1, KDM4B, RAD21, NDRG1, HDGF, CENPA, ACTB, SF3A2, ARRB1, ARRB2, ERG, ISG15, NFX1, CUL3, CUL5, CUL2, CDK2, CUL1, COPS5, DCUN1D1, CAND1, NEDD8, GRK5, INPPL1, GRB2, UBXN6, HNRNPK, HNRNPA1, YBX1, EFTUD2, SRSF1, SNRPA1, HNRNPA3, SNRPD1, PRPF8, SNRNP200, SRSF7, PTBP1, U2AF2, U2AF1, SF3A1, PABPC1, NHP2L1, RNPS1, SRSF11, SNRPA, SRSF3, PRPF4, SNRNP70, RPS15A, RPS23, RPL19, RPL6, RPL7A, RPL18, RPS13, RSL1D1, RPS6, RPL7, RPL12, RPS2, RPL18A, RPLP0, RPL23A, EIF4A3, RPS3, NONO, RPS26, TRA2B, RPS4X, HNRNPA0, UPF1, RPS11, RPS24, RPL5, RPLP1, RALY, SART1, RPS16, RPS8, SRRM2, RPLP2, NOP58, RPS14, RPL30, SMU1, USP39, MCM5, LUC7L3, SAP18, EIF6, MYH9, IK, NOP2, THRAP3, GTF3C1, WDR18, MRPS16, FTSJ3, RRS1, LAMP2, TPBG, MRPL52, RRP7A, TRIM55, MRPL42, PCDHA2, NFIA, MRPS34, KRT3, MARCKS, UTP14A, SEPT7, LBR, PDHA2, TRA2A, PRPH, LIMS1, MRPS28, MTCH1, MTCH2, SLC7A5, PGRMC1, RFC4, ATP6V1B1, LAPTM4A, VTN, TMX2, RHOB, KIAA2013, MRPL23, PCDH7, NCSTN, RPL10L, SND1, PTCD1, MRPL44, MRPL48, ZC3H18, ICT1, ITGB4, PTPN1, MRPL51, LMAN1, TPR, SLC25A17, SEPT2, VDAC2, KRT14, ITGA5, MRPL10, LSM14A, S100A9, MRPL13, WBSCR16, SLC25A32, MAGOH, SMURF1, PNKP, FN1, VCAM1, SYNCRIP, HNRNPD, HNRNPH3, IFIT3, IL7R, MAP1LC3A, UBL4A, ITGA4, DHX9, ZNF689, PAN2, CD81, IGSF8, ICAM1, ADRB2, BAG3, CDKN2A, TARDBP, PARK2, TCERG1, PRPF40A, WBP4, GAS7, NEDD4, PIN1, G3BP1, ABCF1, C14orf166, NELFB, YBX3, DDX1, DIMT1, EIF2B2, EIF2B3, EIF3C, EIF3D, FKBP3, FUS, IGF2BP3, ILF2, KRT18, NMT1, RPL35, RPS27, RPS29, MRE11A, SHFM1, RPA3, RPA2, RPA1, WWOX, HSPA5, UBASH3B, LGR4, IVNS1ABP, MDM2, AURKA, AURKB, CEP250, CEP57, HAUS2, CEP70, CEP76, LGALS3BP, MAGED2, NEDD1, TP53, TUBG1, TUBGCP3, TUBGCP4, HUWE1, FBXW11, KAT2B, PHF6, CUL7, OBSL1, CCDC8, UBE2I, EED, RNF2, TXNDC16, PRMT8, RPS6KB2, HSPB1, UNK, NTRK1, CALR, ATP5A1, BTF3L4, EIF3J, HSPA9, MATR3, MDC1, PDCD6, RAB2A, RPL22, RPS25, RPS3A, SAFB, SLC25A5, SMEK2, TRIP10, WRAP53, HSP90B1, PSMD6, RPN1, SCARNA22, PTEN, AHSA1, CACNA2D1, CHD1, DDX5, EIF2B1, ERCC6, FBL, HIST1H1B, HNRNPA2B1, HNRNPAB, HNRNPC, HNRNPL, RPL10, EXOSC4, MRPL50, CDKN2AIP, HSD17B4, IFI16, IGHMBP2, ILF3, RPSA, RPL10A, NVL, EXOSC10, RFC1, RFC2, RFC3, RFC5, RPL3, RPL4, RPL8, RPL9, RPL11, RPL13, RPL15, RPL17, RPL21, RPL24, RPL27, RPL27A, RPL28, RPL32, RPL36A, RPS5, RPS7, RPS9, RPS10, RPS12, RPS15, RPS17, RPS18, RPS19, RPS21, SRP72, SURF6, TOP2A, TPD52, UBA52, UBTF, DAP3, HIST1H2BL, SMARCA5, PABPC4, DDX18, EIF2B4, H1FX, BAZ1B, DDX21, RPL23, TTC37, PHF14, ESPL1, KIAA0020, HNRNPDL, CEBPZ, ALYREF, HNRNPR, NPM3, MYBBP1A, RPP38, TBL3, IGF2BP1, WDR3, POP1, EBNA1BP2, KRR1, SUPT16H, XRN2, DHX30, PDCD11, RBM34, RRP1B, MRPS27, PHF8, METAP1, FAM120A, RRP12, LARP1, RPL13A, GTPBP4, C3orf17, RPL36, SPATS2L, SERBP1, NOC2L, FBXL6, GNL3, AATF, MRPL46, TRUB2, STAU2, C19orf53, UHRF1, GNL2, PKN3, HP1BP3, RRP15, FCF1, UTP18, MRPS2, MRTO4, HERC5, DDX47, MRPL27, NIP7, RTCB, ESF1, MRPS33, DHX29, GNL3L, GTPBP2, FOCAD, FAM120C, CDCA4, RBM28, SRBD1, NAT10, BRIX1, LYAR, DDX27, TSR1, RIOK2, NKRF, MEPCE, BCCIP, PNO1, DHX33, DDX24, AVEN, REXO4, THAP11, CBX8, USP36, MRPS35, EEFSEC, MRPS14, NOC3L, MRPS25, DDX31, YTHDC2, C12orf43, MRPS15, MRPS9, MRPL38, NBEAL1, NOL6, KRI1, SPATS2, DDX50, DDX54, CCDC86, C14orf169, MUS81, PRR3, TRMT1L, C18orf21, UTP23, GLYR1, MINA, LTV1, SAMD1, ZNF622, TADA1, KRBA2, WDR36, RPP25L, EME1, CENPV, POC1B, CCDC137, GAN, CRY1, UBQLN2, MACROD1, TRIM29, MCM2, CDC5L, SHC1, RC3H1, CRBN, NCL, CYLD, TRIM25, CENPW, BRCA1, LMNA, MTF1, RNF169, HDAC6SLC36A4


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for HNRNPU_SLC36A4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for HNRNPU_SLC36A4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource