DreEX0023085 @ danRer10

Exon Skipping

Gene

ENSDARG00000012405 | col1a1a

Description

collagen, type I, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9102]

Coordinates

chr3:23103287-23104136:+

Coord C1 exon

chr3:23103287-23103394

Coord A exon

chr3:23103503-23103556

Coord C2 exon

chr3:23104029-23104136

Length

54 bp

Sequences

Splice sites

3' ss Seq

TATATTTTTCTTTACATTAGGGT

3' ss Score

8.26

5' ss Seq

AAGGTGAAC

5' ss Score

5.54

Exon sequences

Seq C1 exon

GGAGAGATTGGCAAACAGGGACCTTCTGGTCCATCTGGTGAACGTGGACCTCCTGGCCCCATGGGACCCCCTGGACTGGCTGGACCTCCTGGTGAGCCTGGTCGTGAG

Seq A exon

GGTACTCCAGGAAATGAGGGCTCTGCTGGACGTGACGGTGCTGCTGGCCCCAAG

Seq C2 exon

GGACCCGCTGGAGCTCGTGGAGACAAGGGTGAGACTGGTGAGGCTGGTGAGAGAGGCATGAAGGGACACAGAGGATTCACTGGAATGCCAGGACCCCCTGGTCCTCCT

VastDB Features

Vast-tools module Information

Secondary ID

ENSDARG00000012405_MULTIEX1-35/40=34-38

Average complexity

C3

Mappability confidence:

100%=100=100%

Protein Impact

Alternative protein isoforms (Ref)

No structure available

Features

Disorder rate (Iupred):

C1=1.000 A=1.000 C2=1.000

Domain overlap (PFAM):

C1:

PF0139113=Collagen=PD(12.8=33.3),PF0139113=Collagen=FE(40.7=100)

A:

PF0139113=Collagen=FE(19.8=100),PF0139113=Collagen=PU(16.5=77.8)

C2:

PF0139113=Collagen=PD(17.6=41.7),PF0139113=Collagen=FE(50.7=100)

Main Inclusion Isoform:

ENSDARP00000003177

Main Skipping Isoform:

NA

Other Inclusion Isoforms:

ENSDARP00000047009

Other Skipping Isoforms:

NA

Conservation

Human

(hg38)

chr17:50188742-50188795

HIGH PSI

HsaEX0016380

(COL1A1)

Human

(hg19)

chr17:48266103-48266156

HIGH PSI

HsaEX0016380

(COL1A1)

Mouse

(mm10)

chr11:94948543-94948596

MmuEX6088967

(Col1a1)

Mouse

(mm9)

chr11:94809857-94809910

HIGH PSI

MmuEX6088967

(Col1a1)

Rat

(rn6)

chr10:82758412-82758446

HIGH PSI

RnoEX0022996

(Col1a1)

Cow

(bosTau6)

chr19:37101105-37101158

HIGH PSI

BtaEX6087918

(COL1A1)

Chicken

(galGal4)

chrUn_JH375554:82288-82341

Chicken

(galGal3)

chrUn_random:31476304-31476357

HIGH PSI

GgaEX6047842

(COL2A1)

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

GTCCATCTGGTGAACGTGGAC

R:

TCCCTTCATGCCTCTCTCACC

Band lengths:

146-200

Functional annotations

(Submit an annotation)

There are 0 annotated functions for this event

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

Special

DreEX0023085 @ danRer10

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]