GgaEX1016964 @ galGal4

Exon Skipping

Gene

ENSGALG00000005811 | COL7A1

Description

collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]

Coordinates

chr12:9074846-9081360:+

Coord C1 exon

chr12:9074846-9074890

Coord A exon

chr12:9074980-9075006

Coord C2 exon

chr12:9081319-9081360

Length

27 bp

Sequences

Splice sites

3' ss Seq

TTCCCCCTCTTTTCTTTCAGGGC

3' ss Score

13.69

5' ss Seq

GCTGTAAGC

5' ss Score

4.47

Exon sequences

Seq C1 exon

GGCATTCCCGGAGCACCTGGCACCAAGGGTGACCGTGGGGAGCCG

Seq A exon

GGCCCCCCTGGACTCCCAGGACGAGCT

Seq C2 exon

GGTGAGCCGGCGCTGCTGGAGGGCGTGCTGCTGGGTGAACCC

VastDB Features

Vast-tools module Information

Secondary ID

ENSGALG00000005811_MULTIEX2-24/78=23-56

Average complexity

C2

Mappability confidence:

97%=100=97%

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=FE(20.9=100)

A:

PF0139113=Collagen=FE(11.9=100)

C2:

PF0139113=Collagen=PD(6.9=28.6),PF0139113=Collagen=PU(5.8=21.4)

Main Inclusion Isoform:

ENSGALP00000009317

Main Skipping Isoform:

NA

Other Inclusion Isoforms:

NA

Other Skipping Isoforms:

NA

Other assemblies

galGal3

Conservation

Human

(hg38)

chr3:48579890-48579916

Human

(hg19)

chr3:48617323-48617349

Mouse

(mm10)

chr9:108968994-108969020

Mouse

(mm9)

chr9:108870922-108870948

HIGH PSI

MmuEX6069104

(Col7a1)

Rat

(rn6)

No conservation detected

Cow

(bosTau6)

chr22:51874858-51874884

HIGH PSI

BtaEX6095680

(COL7A1)

Zebrafish

(danRer10)

No conservation detected

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

GCATTCCCGGAGCACCTG

R:

GGTTCACCCAGCAGCACG

Band lengths:

85-112

Functional annotations

(Submit an annotation)

There are 0 annotated functions for this event

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

Special

GgaEX1016964 @ galGal4

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]