GgaINT1009986 @ galGal4
Intron Retention
Gene
ENSGALG00000016155 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2196]
Coordinates
chr3:82324317-82324500:-
Coord C1 exon
chr3:82324450-82324500
Coord A exon
chr3:82324362-82324449
Coord C2 exon
chr3:82324317-82324361
Length
88 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
TTTTAAATTTGCTATTACAGGGA
3' ss Score
7.83
Exon sequences
Seq C1 exon
GGTGTTCCTTACAATGAAAGAAATGGAATGAGCAGCTTATATAAACTCCAG
Seq A exon
GTATTTCTGGTATTTCTTTCTAATATACATAGTTTTTCAATCAACACCTAATTTAGGTCCAACTTAATTTTTAAATTTGCTATTACAG
Seq C2 exon
GGAGGTGCAAGTGTCACAAGTTATCCAGGTCCACCAGGACCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016155:ENSGALT00000026059:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.3=29.4)
A:
NA
C2:
PF0139113=Collagen=PU(13.1=53.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGTTCCTTACAATGAAAGAAATGG
R:
TGGTGGACCTGGATAACTTGTG
Band lengths:
87-175
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]