Motif databaseΒΆ

The RBPs and motifs available in RBPBench are based on the curated list of human RBP binding motifs based on the catRAPID omics database. At present RBPBench hosts 605 RBP binding motifs from 259 RBPs, including 604 MEME/DREME XML based sequence motifs and one covariance model based structure motif. Optionally, the user can add own motifs (user motifs) to the search, or define a custom motif database. The list of current database RBPs and number of motifs per RBP are given below:

RBP

Number of motifs

A1CF

2

ACIN1

2

ACO1

1

ADAR

4

AGGF1

2

AGO1

1

AGO2

2

AKAP1

1

AKAP8

1

ANKHD1

1

AUH

2

BCCIP

1

BOLL

3

BUD13

4

CAPRIN1

1

CBX7

1

CDC40

2

CELF1

1

CELF2

2

CELF4

1

CELF5

1

CELF6

1

CNBP

2

CNOT4

1

CPEB1

1

CPEB2

1

CPEB4

1

CPSF6

1

CPSF7

1

CSTF2

2

CSTF2T

2

DAZ3

4

DAZAP1

4

DDX3X

2

DDX6

1

DDX19B

1

DDX24

2

DDX54

2

DDX55

6

DDX58

1

DDX59

1

DGCR8

1

DKC1

3

EFTUD2

1

EIF3D

5

EIF4A3

3

EIF4B

1

EIF4G2

4

ELAVL1

4

ELAVL2

4

ELAVL3

3

ELAVL4

3

ENOX1

1

ERI1

1

ESRP1

3

ESRP2

1

EWSR1

2

FAM120A

3

FASTKD2

3

FBL

1

FIP1L1

2

FMR1

5

FTO

2

FUBP1

3

FUBP3

2

FUS

2

FXR1

2

FXR2

5

G3BP1

2

G3BP2

1

GNL3

2

GPKOW

2

GRSF1

2

GRWD1

2

GTF2F1

1

HLTF

1

HNRNPA0

2

HNRNPA1

7

HNRNPA1L2

1

HNRNPA2B1

4

HNRNPA3

1

HNRNPAB

3

HNRNPC

2

HNRNPCL1

1

HNRNPD

3

HNRNPDL

3

HNRNPF

1

HNRNPH1

1

HNRNPH2

1

HNRNPK

2

HNRNPL

5

HNRNPLL

2

HNRNPM

5

HNRNPU

6

HNRNPUL1

4

IFIH1

1

IGF2BP1

4

IGF2BP2

2

IGF2BP3

1

IGHMBP2

1

ILF2

2

ILF3

3

KHDRBS1

2

KHDRBS2

1

KHDRBS3

2

KHSRP

5

LARP4

3

LARP4B

1

LIN28A

1

LIN28B

1

LSM11

4

MATR3

1

MBNL1

5

METAP2

1

MSI1

4

MSI2

1

MTPAP

2

NCBP2

3

NELFE

2

NKRF

3

NOL12

2

NONO

2

NOP56

1

NOP58

1

NOVA1

1

NOVA2

4

NPM1

2

NSUN2

2

NUMA1

1

NUP42

2

NXF1

1

OAS1

1

OBI1

1

PABPC1

3

PABPC3

1

PABPC4

1

PABPC5

1

PABPN1

1

PABPN1L

1

PARP1

2

PCBP1

7

PCBP2

9

PCBP4

2

PPIE

2

PPIG

2

PPIL4

5

PPRC1

1

PRPF8

3

PRR3

2

PTBP1

5

PTBP2

1

PTBP3

1

PUF60

1

PUM1

3

PUM2

5

QKI

8

RALY

1

RALYL

1

RANGAP1

1

RBFOX1

4

RBFOX2

2

RBFOX3

1

RBM3

1

RBM4

2

RBM4B

3

RBM5

3

RBM6

1

RBM8A

1

RBM10

2

RBM14

1

RBM15

1

RBM15B

2

RBM22

7

RBM23

2

RBM24

1

RBM25

4

RBM28

1

RBM39

1

RBM41

1

RBM42

1

RBM45

5

RBM46

1

RBM47

1

RBMS1

1

RBMS2

1

RBMS3

5

RBMX

2

RBMY1A1

1

RC3H1

2

TROVE2

7

RPS5

2

SAFB2

2

SAMD4A

1

SART3

1

SF1

2

SF3A3

4

SF3B4

2

SFPQ

6

SLTM

1

SMNDC1

2

SND1

5

SNRNP70

1

SNRPA

3

SNRPB2

1

SOX2

1

SRP14

1

SRP68

1

SRRM4

2

SRSF1

11

SRSF2

8

SRSF3

4

SRSF4

2

SRSF5

5

SRSF6

4

SRSF7

10

SRSF8

2

SRSF9

1

SRSF10

5

SRSF11

2

SSB

1

SUB1

2

SUGP2

2

SUPV3L1

2

SYNCRIP

1

TAF15

5

TARBP2

3

TARDBP

3

TBRG4

2

TIA1

1

TIAL1

2

TNRC6A

2

TRA2A

5

TRA2B

2

TRNAU1AP

2

TUT1

2

U2AF1

4

U2AF2

3

UCHL5

3

UNK

3

UPF1

1

WDR33

1

XPO5

3

XRCC6

4

XRN2

3

YBX1

3

YBX2

1

YBX3

1

YTHDC1

1

YWHAG

1

ZC3H10

1

ZCRB1

1

ZFP36

2

ZFP36L2

2

ZNF184

1

ZNF326

3

ZNF622

3

ZNF638

1

ZRANB2

4

SLBP

1