GgaEX1016959 @ galGal4

Exon Skipping

Gene

ENSGALG00000005811 | COL7A1

Description

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

Coordinates

chr12:9074078-9081360:+

Coord C1 exon

chr12:9074078-9074113

Coord A exon

chr12:9074219-9074299

Coord C2 exon

chr12:9081319-9081360

Length

81 bp

Sequences

Splice sites

3' ss Seq

CCTGACTCTTTCCCCCCCAGGGT

3' ss Score

11

5' ss Seq

GAGGTAGCG

5' ss Score

5.65

Exon sequences

Seq C1 exon

GGCATCACTGGCCTCACTGGCAGGAGTGGCCCCAAG

Seq A exon

GGTGACGCAGGGGAGCCGGGTGAGAAGGGTGAGCCAGGCAGAGTGGGTGCACCAGGACAACCAGGGCAGCGTGGCAAGGAG

Seq C2 exon

GGTGAGCCGGCGCTGCTGGAGGGCGTGCTGCTGGGTGAACCC

VastDB Features

Vast-tools module Information

Secondary ID

ENSGALG00000005811_MULTIEX2-19/78=18-56

Average complexity

C3

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=PU(11.8=66.7)

A:

PF0139113=Collagen=FE(31.0=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)

chr3:48581260-48581340

HIGH PSI

HsaEX6055799

(COL7A1)

Human

(hg19)

chr3:48618693-48618773

HIGH PSI

HsaEX6055799

(COL7A1)

Mouse

(mm10)

chr9:108967605-108967685

HIGH PSI

MmuEX6069109

(Col7a1)

Mouse

(mm9)

chr9:108869650-108869730

HIGH PSI

MmuEX6069109

(Col7a1)

Rat

(rn6)

chr8:117709282-117709362

HIGH PSI

RnoEX6037784

(Col7a1)

Cow

(bosTau6)

chr22:51873622-51873702

HIGH PSI

BtaEX6095685

(COL7A1)

Zebrafish

(danRer10)

chr6:40230702-40230755

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

GCATCACTGGCCTCACTGG

R:

GGTTCACCCAGCAGCACG

Band lengths:

76-157

Functional annotations

(Submit an annotation)

There are 0 annotated functions for this event

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

Special

GgaEX1016959 @ galGal4

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]