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Table 3 List of RNA binding proteins associated with region 36 of the Lif 3′UTR

From: Expression of leukemia inhibitory factor in Müller glia cells is regulated by a redox-dependent mRNA stability mechanism

Protein ID

 

Protein name

Gene name

36 wt versus 36-No Significance

36 wt versus 36-No Rel. levels

Q13126

 

S-methyl-5-thioadenosine phosphorylase

MTAP

6.70E-06

2.11

Q9Y3U8

 

60S ribosomal protein L36

RPL36

1.43E-05

2.05

P30040

 

Endoplasmic reticulum resident protein 29

ERP29

8.03E-05

1.91

P62942

 

Peptidyl-prolyl cis-trans isomerase FKBP1A

FKBP1A

0.0003

1.80

Q14019

 

Coactosin-like protein

COTL1

0.0005

1.76

O75390

 

Citrate synthase, mitochondrial

CS

0.0012

1.68

P15121

 

Aldose reductase

AKR1B1

0.0015

1.66

Q9Y281

 

Cofilin-2

CFL2

0.0019

1.64

Q02543

60S ribosomal protein L18a

RPL18A

0.0020

1.64

P30041

 

Peroxiredoxin-6

PRDX6

0.0022

1.63

P42766

60S ribosomal protein L35

RPL35

0.0024

1.62

Q96AG4

 

Leucine-rich repeat-containing protein 59

LRRC59

0.0041

1.57

Q01130

Serine/arginine-rich splicing factor 2

SRSF2

0.0051

1.55

P26447

 

Protein S100-A4

S100A4

0.0080

1.51

P60059

 

Protein transport protein Sec61 subunit gamma

SEC61G

0.0089

1.50

Q96AE4

Far upstream element-binding protein 1

FUBP1

0.0090

1.50

P09493

 

Tropomyosin alpha-1 chain

TPM1

0.0099

1.49

P40616

 

ADP-ribosylation factor-like protein 1

ARL1

0.0104

1.48

Q99536

 

Synaptic vesicle membrane protein VAT-1 homolog

VAT1

0.0115

1.47

P84098

60S ribosomal protein L19

RPL19

0.0120

1.47

P61019

 

Ras-related protein Rab-2A

RAB2A

0.0127

1.47

Q9HAV7

 

GrpE protein homolog 1, mitochondrial

GRPEL1

0.0127

1.47

O43396

 

Thioredoxin-like protein 1

TXNL1

0.0136

1.46

P26639

 

Threonine--tRNA ligase, cytoplasmic

TARS

0.0137

1.46

P09972

 

Fructose-bisphosphate aldolase C

ALDOC

0.0143

1.45

Q01581

 

Hydroxymethylglutaryl-CoA synthase, cytoplasmic

HMGCS1

0.0144

1.45

P63261

 

Actin, cytoplasmic 2; Actin, cytoplasmic 2, N-terminally processed

ACTG1

0.0152

1.45

Q99497

Protein DJ-1

PARK7

0.0180

1.43

P16989

DNA-binding protein A

CSDA

0.0192

1.42

P06748

Nucleophosmin

NPM1

0.0212

1.41

Q9BTT0

 

Acidic leucine-rich nuclear phosphoprotein 32 family member E

ANP32E

0.0221

1.41

P39023

60S ribosomal protein L3

RPL3

0.0227

1.41

P13693

 

Translationally-controlled tumor protein

TPT1

0.0267

1.39

P41567

Eukaryotic translation initiation factor 1

EIF1

0.0270

1.39

P49207

60S ribosomal protein L34

RPL34

0.0290

1.38

Q9Y266

 

Nuclear migration protein nudC

NUDC

0.0305

1.38

Q15020

Squamous cell carcinoma antigen recognized by T-cells 3

SART3

0.0331

1.37

P09429

 

High mobility group protein B1; Putative high mobility group protein B1-like 1

HMGB1

0.0364

1.36

P40429

 

60S ribosomal protein L13a; Putative 60S ribosomal protein L13a-like

RPL13A

0.0365

1.36

O43747

 

AP-1 complex subunit gamma-1

AP1G1

0.0400

1.35

Q00577

 

Transcriptional activator protein Pur-alpha

PURA

0.0410

1.35

P27635

 

60S ribosomal protein L10

RPL10

0.0414

1.34

P00558

 

Phosphoglycerate kinase 1

PGK1

0.0462

1.33

P22314

 

Ubiquitin-like modifier-activating enzyme 1

UBA1

0.0473

1.33

Q9H0U4

 

Ras-related protein Rab-1B

RAB1B

0.0475

1.33

P61106

Ras-related protein Rab-14

RAB14

0.0495

1.32

P49588

 

Alanine--tRNA ligase, cytoplasmic

AARS

0.0503

1.32

O75915

PRA1 family protein 3

ARL6IP5

0.0505

1.32

P55795

 

Heterogeneous nuclear ribonucleoprotein H2

HNRNPH2

0.0523

1.32

P30086

 

Phosphatidylethanolamine-binding protein 1; Hippocampal cholinergic neurostimulating peptide

PEBP1

0.0533

1.32

P68036

 

Ubiquitin-conjugating enzyme E2 L3

UBE2L3

0.0580

1.31

Q9UQE7

 

Structural maintenance of chromosomes protein 3

SMC3

0.0583

1.31

  1. RNAs of region 36 (‘R36 wt’) and its counterpart ARE-null region 36 (‘R36-No’) were used for RNA binding assays. Bound proteins were identified by quantitative mass spectrometry analysis and relative ratios were determined using total sequence reads for region ‘R36 wt’ and region ‘R36-No’. RNA binding proteins (stars) are indicated as identified by GO pathway analysis (see Additional file 7: File S2). The significance is the significance A P-value as determined by the Perseus software, defining the likelihood of a protein being enriched compared to the background distribution.