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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: 32551

FusionGeneSummary for SAFB2_KHSRP

check button Fusion gene summary
Fusion gene informationFusion gene name: SAFB2_KHSRP
Fusion gene ID: 32551
HgeneTgene
Gene symbol

SAFB2

KHSRP

Gene ID

9667

8570

Gene namescaffold attachment factor B2KH-type splicing regulatory protein
Synonyms-FBP2|FUBP2|KSRP
Cytomap

19p13.3

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionscaffold attachment factor B2far upstream element-binding protein 2FUSE-binding protein 2p75
Modification date2018052320180527
UniProtAcc

Q14151

Q92945

Ensembl transtripts involved in fusion geneENST00000252542, ENST00000591310, 
ENST00000398148, 
Fusion gene scores* DoF score6 X 6 X 6=2162 X 2 X 2=8
# samples 72
** MAII scorelog2(7/216*10)=-1.6256044852185
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: SAFB2 [Title/Abstract] AND KHSRP [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
* 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
TgeneKHSRP

GO:0043488

regulation of mRNA stability

16126846

TgeneKHSRP

GO:0045019

negative regulation of nitric oxide biosynthetic process

16126846

TgeneKHSRP

GO:0061014

positive regulation of mRNA catabolic process

16126846

TgeneKHSRP

GO:0061158

3'-UTR-mediated mRNA destabilization

16126846


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
TCGARVPRADTCGA-EJ-5515-01ASAFB2chr19

5616143

-KHSRPchr19

6418090

-
* 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
In-frameENST00000252542ENST00000398148SAFB2chr19

5616143

-KHSRPchr19

6418090

-
intron-3CDSENST00000591310ENST00000398148SAFB2chr19

5616143

-KHSRPchr19

6418090

-

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FusionProtFeatures for SAFB2_KHSRP


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SAFB2

Q14151

KHSRP

Q92945

Binds to scaffold/matrix attachment region (S/MAR) DNA.Can function as an estrogen receptor corepressor and can alsoinhibit cell proliferation. Binds to the dendritic targeting element and may play arole in mRNA trafficking (By similarity). Part of a ternarycomplex that binds to the downstream control sequence (DCS) of thepre-mRNA. Mediates exon inclusion in transcripts that are subjectto tissue-specific alternative splicing. May interact with single-stranded DNA from the far-upstream element (FUSE). May activategene expression. Also involved in degradation of inherentlyunstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly by recruiting degradation machinery to ARE-containing mRNAs. {ECO:0000250, ECO:0000269|PubMed:11003644,ECO:0000269|PubMed:8940189, ECO:0000269|PubMed:9136930}.

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
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-42130_64181954DomainSAP
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820498_612293712Compositional biasNote=Ala/Gly/Pro-rich
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820322_386293712DomainKH 3
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820424_491293712DomainKH 4
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820571_684293712RegionNote=4 X 12 AA imperfect repeats
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820571_582293712RepeatNote=1
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820617_628293712RepeatNote=2
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820643_654293712RepeatNote=3
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820673_684293712RepeatNote=4

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421482_545181954Compositional biasNote=Lys-rich
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421619_724181954Compositional biasNote=Glu-rich
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421621_788181954Compositional biasNote=Arg-rich
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421792_926181954Compositional biasNote=Gly-rich
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421407_485181954DomainRRM
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421713_730181954MotifNuclear localization signal
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-82068_496293712Compositional biasNote=Gly-rich
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-8207_67293712Compositional biasNote=Gly/Pro-rich
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820144_208293712DomainKH 1
TgeneKHSRPchr19:5616143chr19:6418090ENST00000398148-820233_299293712DomainKH 2


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FusionGeneSequence for SAFB2_KHSRP


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.
>In-frame_SAFB2_ENST00000252542_chr19_5616143_-_KHSRP_ENST00000398148_chr19_6418090_-_600aa
MAETLPGSGDSGPGTASLGPGVAETGTRRLSELRVIDLRAELKKRNLDTGGNKSVLMERLKKAVKEEGQDPDEIGIELEATSKKSAKRCV
KGLKMEEEGTEDNGLEDDSRDGQEDMEASLENLQNMGMMDMSVLDETEVANSSAPDFGEDGTDGLLDSFCDSKEYVAAQLRQLPAQPPEH
AQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHA
ARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNF
KLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPGPFNQGPPGAPPHAGGPPPHQYPPQGWGNTYPQWQPPAPHDP
SKAAAAAADPNAAWAAYYSHYYQQPPGPVPGPAPAPAAPPAQGEPPQPPPTGQSDYTKAWEEYYKKIGQQPQQPGAPPQQDYTKAWEEYY


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_SAFB2_ENST00000252542_chr19_5616143_-_KHSRP_ENST00000398148_chr19_6418090_-_1800nt
ATGGCGGAGACTCTGCCCGGGTCGGGCGACTCGGGCCCTGGCACGGCTTCTCTCGGCCCGGGCGTTGCGGAGACTGGGACGAGGCGGCTC
AGCGAGCTGCGGGTGATCGATCTGCGGGCGGAGCTGAAGAAGCGGAACCTGGACACGGGCGGCAACAAGAGCGTCCTGATGGAGCGGCTC
AAGAAGGCGGTTAAAGAAGAGGGGCAAGATCCTGATGAAATTGGCATCGAGTTAGAAGCCACCAGCAAGAAGTCAGCCAAGAGATGTGTT
AAAGGACTGAAGATGGAGGAGGAAGGCACAGAAGATAATGGCCTGGAAGACGATTCCAGAGACGGGCAGGAGGACATGGAAGCAAGTCTG
GAGAACCTGCAGAATATGGGCATGATGGACATGAGTGTGCTAGACGAAACTGAAGTGGCGAATAGCAGTGCTCCAGATTTTGGGGAGGAT
GGCACGGACGGCCTTCTCGATTCCTTTTGTGATAGTAAAGAATACGTGGCTGCACAGCTGAGACAGCTCCCGGCTCAGCCCCCAGAGCAT
GCTCAAGCCTGTGAGATGGTGATGGACATCCTCCGGGAACGTGACCAAGGCGGCTTTGGGGACCGGAATGAGTACGGATCTCGGATTGGC
GGAGGCATCGATGTGCCAGTGCCCAGGCATTCTGTTGGCGTGGTCATTGGCCGGAGTGGAGAGATGATCAAGAAGATCCAGAATGATGCT
GGCGTGCGGATACAGTTCAAGCAAGATGACGGGACAGGGCCCGAGAAGATTGCTCATATAATGGGGCCCCCAGACAGGTGCGAGCACGCA
GCCCGGATCATCAACGACCTCCTCCAGAGCCTCAGGAGTGGTCCCCCAGGTCCTCCAGGGGGTCCAGGCATGCCCCCGGGGGGCCGAGGC
CGAGGAAGAGGCCAAGGCAATTGGGGTCCCCCTGGCGGGGAGATGACCTTCTCCATCCCCACTCACAAGTGTGGGCTGGTCATCGGCCGA
GGTGGCGAGAATGTGAAAGCCATAAACCAGCAGACGGGAGCCTTCGTAGAGATCTCCCGGCAGCTGCCACCCAACGGGGACCCCAACTTC
AAGTTGTTCATCATCCGGGGTTCACCCCAGCAGATTGACCACGCCAAGCAGCTTATCGAGGAAAAGATCGAGGGTCCTCTCTGCCCAGTT
GGACCAGGCCCAGGTGGCCCAGGCCCTGCTGGCCCAATGGGGCCCTTCAATCCTGGGCCCTTCAACCAGGGGCCACCCGGGGCTCCCCCA
CATGCCGGGGGGCCCCCTCCTCACCAGTACCCACCCCAGGGCTGGGGCAATACCTACCCCCAGTGGCAGCCGCCTGCTCCTCATGACCCA
AGCAAAGCAGCTGCAGCGGCCGCGGACCCCAACGCCGCGTGGGCCGCCTACTACTCACACTACTACCAGCAGCCCCCGGGCCCCGTCCCC
GGCCCCGCACCGGCCCCTGCGGCCCCACCGGCTCAGGGTGAGCCCCCTCAGCCCCCACCCACCGGCCAGTCGGACTACACTAAGGCCTGG
GAAGAGTATTACAAAAAGATCGGCCAGCAGCCCCAGCAGCCCGGAGCACCCCCACAGCAGGACTACACGAAGGCTTGGGAGGAGTACTAC
AAGAAGCAAGCGCAAGTGGCCACCGGAGGGGGTCCAGGAGCTCCCCCAGGCTCCCAGCCAGACTACAGTGCCGCCTGGGCGGAATATTAC
AGACAGCAGGCCGCTTACTACGGACAGACCCCAGGTCCTGGCGGCCCCCAGCCGCCGCCCACGCAGCAGGGACAGCAGCAGGCTCAATGA


* Fusion transcript sequences (Full-length transcript).
>In-frame_SAFB2_ENST00000252542_chr19_5616143_-_KHSRP_ENST00000398148_chr19_6418090_-_2829nt
CTCCCGCCGGGAACTGCCGGGACGCATGCGAGCTGCAGATTCAGCGCTTGCGCGTTGTGCCGGGGAACCCGCGGTTGGTGGACGCGCGAG
CGTCCTTGCTGCTAAGTACGCTAGTGGGGGCGGTGCGCGTGCGCGTGCGCGGCCGCAAAGCGGGGCGGGAGGAAACGAGTGCGTTTTCCT
CTTAGGCGGCGCCATTTTGTGTTCAGAGCCGCTATAGCTGCCGGCGGTGTGCGACTGAGTCGGTGGCGAAGACGGGAACGCGACGATGGC
GGAGACTCTGCCCGGGTCGGGCGACTCGGGCCCTGGCACGGCTTCTCTCGGCCCGGGCGTTGCGGAGACTGGGACGAGGCGGCTCAGCGA
GCTGCGGGTGATCGATCTGCGGGCGGAGCTGAAGAAGCGGAACCTGGACACGGGCGGCAACAAGAGCGTCCTGATGGAGCGGCTCAAGAA
GGCGGTTAAAGAAGAGGGGCAAGATCCTGATGAAATTGGCATCGAGTTAGAAGCCACCAGCAAGAAGTCAGCCAAGAGATGTGTTAAAGG
ACTGAAGATGGAGGAGGAAGGCACAGAAGATAATGGCCTGGAAGACGATTCCAGAGACGGGCAGGAGGACATGGAAGCAAGTCTGGAGAA
CCTGCAGAATATGGGCATGATGGACATGAGTGTGCTAGACGAAACTGAAGTGGCGAATAGCAGTGCTCCAGATTTTGGGGAGGATGGCAC
GGACGGCCTTCTCGATTCCTTTTGTGATAGTAAAGAATACGTGGCTGCACAGCTGAGACAGCTCCCGGCTCAGCCCCCAGAGCATGCTCA
AGCCTGTGAGATGGTGATGGACATCCTCCGGGAACGTGACCAAGGCGGCTTTGGGGACCGGAATGAGTACGGATCTCGGATTGGCGGAGG
CATCGATGTGCCAGTGCCCAGGCATTCTGTTGGCGTGGTCATTGGCCGGAGTGGAGAGATGATCAAGAAGATCCAGAATGATGCTGGCGT
GCGGATACAGTTCAAGCAAGATGACGGGACAGGGCCCGAGAAGATTGCTCATATAATGGGGCCCCCAGACAGGTGCGAGCACGCAGCCCG
GATCATCAACGACCTCCTCCAGAGCCTCAGGAGTGGTCCCCCAGGTCCTCCAGGGGGTCCAGGCATGCCCCCGGGGGGCCGAGGCCGAGG
AAGAGGCCAAGGCAATTGGGGTCCCCCTGGCGGGGAGATGACCTTCTCCATCCCCACTCACAAGTGTGGGCTGGTCATCGGCCGAGGTGG
CGAGAATGTGAAAGCCATAAACCAGCAGACGGGAGCCTTCGTAGAGATCTCCCGGCAGCTGCCACCCAACGGGGACCCCAACTTCAAGTT
GTTCATCATCCGGGGTTCACCCCAGCAGATTGACCACGCCAAGCAGCTTATCGAGGAAAAGATCGAGGGTCCTCTCTGCCCAGTTGGACC
AGGCCCAGGTGGCCCAGGCCCTGCTGGCCCAATGGGGCCCTTCAATCCTGGGCCCTTCAACCAGGGGCCACCCGGGGCTCCCCCACATGC
CGGGGGGCCCCCTCCTCACCAGTACCCACCCCAGGGCTGGGGCAATACCTACCCCCAGTGGCAGCCGCCTGCTCCTCATGACCCAAGCAA
AGCAGCTGCAGCGGCCGCGGACCCCAACGCCGCGTGGGCCGCCTACTACTCACACTACTACCAGCAGCCCCCGGGCCCCGTCCCCGGCCC
CGCACCGGCCCCTGCGGCCCCACCGGCTCAGGGTGAGCCCCCTCAGCCCCCACCCACCGGCCAGTCGGACTACACTAAGGCCTGGGAAGA
GTATTACAAAAAGATCGGCCAGCAGCCCCAGCAGCCCGGAGCACCCCCACAGCAGGACTACACGAAGGCTTGGGAGGAGTACTACAAGAA
GCAAGCGCAAGTGGCCACCGGAGGGGGTCCAGGAGCTCCCCCAGGCTCCCAGCCAGACTACAGTGCCGCCTGGGCGGAATATTACAGACA
GCAGGCCGCTTACTACGGACAGACCCCAGGTCCTGGCGGCCCCCAGCCGCCGCCCACGCAGCAGGGACAGCAGCAGGCTCAATGAATCGA
ATGAATGTGAACTTCTTCATCTGTGAAAAATCTTTTTTTTTTCCATTTTGTTCTGTTTGGGGGCTTCTGTTTTGTTTGGCGAGAGAGCGA
TGGCTGCCGTGGGGAGTACTGGGGAGCCCTCGCGGCAAGCAGGGTGGGGGGGACTTGGGGGCATGCCGGGCCCTCACTCTCTCGCCTGTT
CTGTGTCTCACATGCTTTTTCTTTCAAAATTGGGATCCTTCCATGTTGAGCCAGCCAGAGAAGATAGCGAGATCTAAATCTCTGCCAAAA
AAAAAAAAAAACTTAAAAATTAAAAACACAAAGAGCAAAGCAGAACTTATAAAATTATATATATATATATTAAAAAGTCTCTATTCTTCA
CCCCCCAGCCTTCCTGAACCTGCCTCTCTGAGGATAAAGCAATTCATTTTCTCCCACCCTCGGCCCTCTTGTTTTTAAAATAAACTTTTA
AAAAGGAAAAAAAAAAGTCACTCTTGCTATTTCTTTTTTTTAGTTAGAGGTGGAACATTCCTTGGACCAGGTGTTGTATTGCAGGACCCC
TTCCCCCAGCAGCCAAGCCCCCTCTTCTCTCCCTCCCGCCCTGGCTCAGCTCCCGCGGCCCCGCCCGTCCCCCCTCCCAGGACTGGTCTG
TTGTCTTTTCATCTGTTCAAGAGGAGATTGAAACTGAAAACAAAATGAGAACAACAAAAAAAATTGTATGGCAGTTTTTACTTTTTATCG


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FusionGenePPI for SAFB2_KHSRP


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
SAFB2SAFB, ESR1, SORBS3, CHGB, MAP1LC3A, RB1CC1, NCOR1, HDAC3, TOPORS, CUL3, COPS5, CAND1, SRCAP, IK, APOA1, FNTA, FUS, GIT2, ZSCAN18, MOV10, CUL7, OBSL1, EZH2, SUZ12, EED, BMI1, TP53, RSPH9, RBMX, FNDC4, ZFP41, HNRNPUL1, CCAR1, SSB, HNRNPA1, MYO1C, PPP1CB, PPP1CC, EMC2, MATR3, MPHOSPH8, CAMKK1, MEX3C, ELAVL2, DHPS, TRIP6, APOBEC3D, CAPN13, CIZ1, CLK3, COX15, VDAC1, G3BP1KHSRPPUF60, EXOSC2, PARN, PTBP2, HNRNPA1, HNRNPH1, A1CF, PSMA3, GSK3B, STK3, GADD45A, ELAVL1, SIRT7, CUL3, CUL4B, CUL5, CUL2, CDK2, CUL1, COPS5, CAND1, NEDD8, RAE1, CPLX1, CIRBP, ASF1B, STRIP1, FN1, VCAM1, UBL4A, ITGA4, MPG, CD81, TARDBP, APBB1, GARS, GFPT1, HNRNPD, ALDH16A1, NAP1L4, WWOX, LGR4, UBC, STAU1, HUWE1, CUL7, OBSL1, CCDC8, SUZ12, EED, RNF2, MAEL, CHCHD2, CPSF6, CPSF7, FUBP3, HTRA2, EIF4B, RAD54L2, SMARCA2, KYNU, NUP50, PRDX2, PRDX5, SIN3A, SMARCC1, SMARCC2, SYMPK, NTRK1, SCARNA22, MKNK2, FOS, JUN, FOXF1, CRY2, MCM2, NANOG, U2AF2, KLHL12, BRCA1, UBE2I, DROSHA, DGCR8, MIRLET7A1, MIRLET7A3


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
HgeneSAFB2chr19:5616143chr19:6418090ENST00000252542-421600_953181954SAFB1


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


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RelatedDrugs for SAFB2_KHSRP


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneKHSRPQ92945DB11638ArtenimolFar upstream element-binding protein 2small moleculeapproved|investigational

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RelatedDiseases for SAFB2_KHSRP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKHSRPC0149925Small cell carcinoma of lung1CTD_human