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Minigene Tables


A minigene is a genomic fragment that includes the alternative exon(s) and the surrounding introns as well as the flanking constitutively spliced exons. Such a minigene is cloned in a eukaryotic expression vector. Thus, the transfected minigene should contain all RNA-elements necessary to show the same alternative splicing pattern as the corresponding endogenous alternatively spliced gene when compared in a specific cellular environment.

Minigene structures and their association with the AEdb-Sequence database are shown in this web document or can be downloaded/viewed as a Microsoft Word document (6.6 Mb). The associated AEdb-Sequence entries and Medline bibliography records are hyperlinked.

The analysis of alternative splicing by minigenes are described in:

  1. Tang, Y., Novoyatleva , T., Benderska, N., Kishore, S., Thanaraj, T.A., and Stamm, S. (2004). Analysis of alternative splicing in vivo using
    minigenes. In Handbook of RNA Biochemistry, Westhof, Bindereif, Schön, and Hartmann, eds. (Wiley-VCH), pp. 755-782.
  2. Stoss, O., Stoilov, P., Hartmann, A.M., Nayler, O., and Stamm, S. The in-vivo minigene approach to analyse tissue-specific splicing. Brain Research Protocols 4: 383-394 (1999) PMID: 10592349.

We are trying to keep this list up to date. If your minigene is missing, please contact Stefan Stamm.

A: minigene containing one casette exon
name species tissue specificity&minigene Cell lines Medline AEdb ID

GABAAγ2

24nt exon

rat

Image

Rat brain, Hela

9292499,

9917071,

8756411

346

Clathrin

light chain B,

exon EN

rat

Image

Primary rat neuronal

cell, rat primary glia cells,p19

9917071,

1408826,

9889339

 

105

src,

exon N1

mouse

Image

Neuronal Lans,neuroblastoma,

Hela,HEK293

9917071,

7474099,

9343417

 

442, 519

NCAM,

Exon 18

mouse

Image

N2A,non muscle fibroblast,myoblast

9582442,

1869048

 

1454

MHC-B,

Exon N30

human

Image

Neuronal retinoblastoma Y79

8663598

1455

Fibronectin

EDI(EDA)

human

Image

Hela

12615332,

8152907

614

Fibronectin

EIIIA

mouse

Image

NIH3T3,Hep3B,HepG2,Hela,N-Mute Mouse liver,LMM3 mouse mammary

8152907,

9804187

 

385

Fibronectin

EIIIB

rat

Image

Human neuroblastoma platt,

murine fibroblast 3T3,F11

8635499,

9632774

 

386

Insulin receptor,

Exon 11

human

Image

HepG2, 3T3L1 adepocytes

9553088

302

NCAM,

Exon MSDb

mouse

Image

Embryonic fibroblasts C3H10T1/2,

bc3H1,

Hela,COS1

9582442

 

799

ccTNT,

Exon5

chicken

Image

Primary skeletal muscles from chicken embryo

9671461,

3419923

 

375

AMP

Deaminase1,

Exon2

rat

Image

3T3,Slo8

 

1922051

 

1456

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

4.1R

murine

Image

MEL cells

11739190

31

CASR

Calcium-sensing receptor

human

Image

HEK293,

Lymphoblastoid cell

11668634

 

1457

Caspase2

human

Image

Hela, 293T

11158574

 

1458

CFTR

human

Image

Hep3B

12421814,

10915765

 

1459

CYP3A5

human

Image

CaCo-2

11502729

 

1460

APP

human

mouse

Image

NIH3T3,P19,N2A,AtT20

10636908

 

1461

hnRNPA1

human

Image

Hela

10982852

 

1462

DUP4-1

β-globin

human

Image

Hela

10982852,

1944277

 

 

DUP4-1

β-globin

human

Image

Hela

10982852,

1944277

 

NMHC-B

human

Image

Y79,Hela

10931847

1455

CD44

/Insulin

mouse

Image

KLN205,LB172.3,HEK293

11118435,

9582284

 

1018

F1-γ

mouse

Image

C2C12,L929

10821853

 

1060

MLH1

human

Image

COS7

11585727

 

1463

NF1

Fibromatosis

Type1

human

Image

Hep3B

12624144

 

1466

SMN

Human

murine

Image

HEK293,NIH3T3,COS1,C2C12,U20S,H9,A9,Hela

10931943,

11726560

 

1467

Spastin

Exon5

human

Image

COS1

11309678

1469

Spastin

Exon9

human

Image

COS1

11309678

1470

Spastin

Exon11

human

Image

COS1

11309678

 

1471

Tau

Exon10

rat

human

Image

Rat PC12(CRL-1721),Rat AR42J(CRL-1492),Monkey COS1(CRL-1650),N2A,Hela RB

11560926,

10805746

 

97

Tau

Exon2

human

Image

SKN,COS,N-Tera2(NT2)

12941465

 

99

Tau

Exon6

human

Image

Chinese Hamster

9523550

 

102

Tau-Exon3/

Insulin

human

mouse

Image

HN10,COS

11118435,

7567473

 

100

UL37

HCMV

Human cytomegalovirus

Image

Human diploid Fribroblasts(HFP)cells

12533698

 

 

CD44

Exon5

mouse

Image

HaCa keratinocytes,HT-3,cervix carcinoma

2574867

 

1018

FGFR-1

Exon α

human

Image

NT-2,JEG-3,T98G,SNB19,glioblastoma cells

8995402

 

1464

Myosin heavy chain exon 18

Droso-phila

Image

Drosophila larvae

1907580

 

1472

FcγRIIA,

Exon Tm

human

Image

Hela, Dami cells Neutrophils

7787414

 

1085

Interleukin3α

Exon 8

mouse

Image

COS,3T3

7889941

 

1473

DHFR,exon2A

Reporter gene

hamster

Image

Chinese Hamster

8417332

1474

HIV-1,

Exon 6D

HIV-1

Image

CEM CD4&T-cell,Hela-Tat

9343212

 

 

SRp20

Exon 4

human

Image

Murine B, lymphoma K46

9305649

 

833

PPT

Exon 4

rat

Image

NIH3T3,P19,N2A,AtT20

1825520

 

1475

apoA-II

exon 3

human

Image

Hep3B

(G29C, A99T, A97T)

15247216

3211

Agtr1a

Exon 2

Norway rat

Image

A10

CHO

15319432

2485

Caspase-2, exon9

human

Image

HeLa, U937, CAM/C2, P388-45R, HL60/MX2

9689050

1458

CD72

exon 8

human

Image

COS-7

15459183

2611

chloride channel 2 (CLCN2), exon3

Homo sapiens

Image

CaCO-2

15252188

3212

cTNT

exon 5

human

Image

QT35

14973222

1284

Fibroblast Growth Factor Receptor 1, exon alpha

human

Image

SNB19, JEG3

15604250

1464

Fibroblast Growth Factor Receptor 2, exon IIIb

rat

Image

AT3, DT3, 293

15126509

110

Fn1   fibronectin 1, exon EIIIA

 

R.norvegicus

 

 

 

 

Image

 

Black boxes indicate Fn exons, and gray boxes indicate α-globin exons. The heavy horizontal lines are intron sequences. The right-angle arrow is the start site of transcription.. The block arrows show the position of the forward and reverse PCR primers (7).

 

sinusoidal endothelial cells (SEC)

15604136

385,

2206

PTB

exon 11

Homo sapiens

Image

HeLa cell

14731397

3201

IKBKAP

Exon/intron 20

human

Image

HEK293

14709595

3045

SMN,exon7

Homo sapiens

Image

293 cells

14667816

1467

Zis minigene

mouse

Image

Hela cell

15524277

3006

Presenilin 2, exon 5

human

brainImage

SK-N-SH cell, neuroblastoma cell,

15569262

3215

HLA-DQB1

 

human

Image

VAVY, MOU MANN, LUY, TUBO, AMALA, BOLETH, YAR, PE117, WT51, BM14, SAVC, MT14B, T7526, LKT3, MADURA, KAS116, AZH, WT52, TEM, E4181324, SCHU, OMW, WT47, KOSE, HO301.

 

 

 

 

 

 

 

 

 

 

 

 

15496424

548

B: minigene containing multiple casette exons

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

Fast sceletal

TnT,

Exon 4-7

rat

Image

COS,Hela,

Nonmuscle cells

3581171

 

374, 375, 376,

378

CD45

Exon4-6

human

mouse

Image

B-cells,

T-cells,

Thymoma cells(EL4,NIH3T3)

1532394,

1692621,

9485182

 

132, 133, 134,

634,

635,

636

spastin

human

Image

COS1

11704932

 

1512,

1513,

1471

CD44

exon v4, v5

Mouse

Image

HeLa

14982999

1019, 1018

GluR-B minigene

mouse

Image

Hela cell

15524277

58,59

C: minigene containing a retained intron

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

bGH

intron D

bovine

Image

CHO

7890647

 

1511

Adenovirus/

Human

tropomyosin

human

Image

COS,HEK293

12384611

 

 

coagulation factor II (thrombin),

intron 13

Homo sapiens

Image

HepG2

Cell line

14504098

3213

D: minigene containing incremental combinatorial exons

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

Tau

Exon2,3

human

Image

COS,SKN,fetal Neurons

7567473

 

99, 100

CD45

mouse

Image

Spleen, B-cells, Thymocytes, T-cells

12393487,

9694517

 

132,

133,

134

E: minigene containing mutually exclusive exons

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

α-tropomyosin

exon 2,3

rat

Image

Muscle and nonmuscle cells

9848651,

2010089,

9837984,

2924347

 

381,

382

αs-tropomyosin

exon NM,SK

human

Image

COS1,myoblasts

1508190

 

1476,

1477

β-tropomyosin

exon 6A,B

chicken

Image

Mouse and quail muscle cells,Hela

8051042,

9130721,

7761834

 

166,

167

β-tropomyosin

exon 6,7

rat

Image

Hela

9622121

 

1478, 1479

Pyruvatekinase M, exon9,10

human

Image

dRLh-84cells and hepatocytes

8631356

 

1480,

1581

Albumin

Exon G,H

rat

Image

Nonhepatic cells,COS1,Hepatoma cells,HLE

8062220

 

1482,

1483,

1484

MLC

Exon 1-4

rat

Image

Hela

2325649

 

1485,

1486,

1487,

1488

FGFR

K-SAM

human

Image

Hela,293

9858549

 

284,

285

APP

Amyloid precursor protein

rat

human

Image

Spleenocytes and thymocytes of mice

12393487,

8917100

 

699,

700

BCR-ABL fusion gene

human

Image

293T,CV1,CML,K562 EM3

10794714

 

1489,

1490

FGF-R2

rat

Image

AT3,DT3

9528792,

10982855

110

GlyRα2

human

Image

293

10829067

 

 

1491

hTra2-β

human

Image

HEK293

11118435,

9790768

 

1492,

1493

β-tropomyosin exon 6B

chicken

Image

HeLa cell

15208309

167

β-tropomyosin exon 6B

chicken

Image

QM7 cell

15208309

167

protein tyrosine phosphatase receptor type C, PTPRC, exon 6

Homo sapiens

Image

Cd4+ AND CD8+

15333587

134, 960

F: minigene containing alternative 3’ splice sites

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

CT/CGRP

human

Image

Hela,CHO,glioblastoma T98G,F9,teratocarcinoma cells

1649451,

9858533,

8463344

 

601,

602

dsx RO

Droso-phila

Image

Drosophila KC cells

1518835

 

1506

M-tra

Droso-phila

Image

Drosophila melanogaster

7761834,

7680770

417,

418,

419

BPV-1

rat

Image

Hela

9826658

 

 

CFTR

human

Image

COS7,IB3

12913074

 

1494

Calcitonin

/DHFR

hamster

Image

293

11477570

601

Calcitonin

With PNP

Human

PNP:Ecoli

Image

MTC,T98G,glioblastoma,HepG2

(hepatoma)

12629124

601

CNV

Nasi/pCV

Droso-phia

Image

Drosophila

11581160,

9666073

1495

Thrombo-poietin

human

Image

Hep3B

11160920

1525

DMD, dystrophin, pseudo exon from intron11

human

The image “http://www.sciencedirect.com/cache/MiamiImageURL/B6WBK-4C4BJHG-J-4/0?wchp=dGLbVzz-zSkWb” cannot be displayed, because it contains errors.

C2C12 (skeletal muscle) myoblasts and myotubes for B; H9C2 cardiomyocytes for C, and HeLa cells for D

15094399

130

G: minigene containing alternative 5’ splice sites

name

species

tissue specificity        minigene

Cell lines

Medline

AEDB ID

E1A

Adenovirus

Image

COS7

8085156

 

 

SERCA2

Exon 2a

hamster

Image

Mouse neuroblastoma derived C1300 derived N2a cells

9645964,

7522437

 

366

Caldesmon

human

Image

COS M6,Hela

7623794

 

1508

SWAP

human

Image

COS7

8940107

 

1509

SV40

t-antigen

human

Image

Hela,293

2163768,

7489505

 

 

β-globin

β-thalassemic allele

human

Image

Hela,Neuron

8085156,

2364434

1510

Fibronectin

Exon IIICS

human

Image

COS7,Hela

7623794,

1478944

 

525, 526, 527

Adenovirus

/human

tropomyosin

human

Image

COS,293

12384611

 

Adenovirus-based

Adenovirus

Image

HeLa

14982999

11094074

 

Doublesex, exon 4 and MS2 hairpin

Drosophila melanogaster

Image

HeLa

15304226

1506

BCL2L1

Exon2

Homo sapiens

Image

K562 cell and U521 cell

15625014

2909

CAD

hamster

Image

translation inhibitor cycloheximide(CHX), pmCMV-Gl-39Ter

15388876

 

TCIRG1, exon 2

Homo sapiens

Image

Hela and Hep3B cell lines

 

15300850

 

TCIRG1,

exon 6

Homo sapiens

Image

Hela and Hep3B cell lines

 

15300850

 

TCIRG1, intron 13

Homo sapiens

Image

Hela and Hep3B cell lines

 

15300850

 

IDUA

human

NAImage

translation inhibitor cycloheximide(CHX), pmCMV-Gl-39Ter

15388876

3214

twintron

Drosophila Melanogaster

An external file that holds a picture, illustration, etc., usually as some form of binary object. The name of referred object is zmb0050414390002.jpg

 

The PRE (purine rich element is in green. Delta is for deletion while R is for replacement.

The PRE lies within the 109 nucleotides sequence downstream from exon 2.

Drosophila Kc cell line. Human HeLa cells.

14966268

 

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