GgaINT1010113 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14056506-14057033:+
Coord C1 exon
chr4:14056506-14056604
Coord A exon
chr4:14056605-14056886
Coord C2 exon
chr4:14056887-14057033
Length
282 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTCTCTTGCACTGTGTGCAGGTC
3' ss Score
8.37
Exon sequences
Seq C1 exon
GTGTCAGAGGTGAGCCTGGTCTCATGGGGATGCCAGGTAAAGATGGGCCTCCAGGGGATCCTGGTTACCCTGGGCAGAAAGGTGGAATGGGACATCGAG
Seq A exon
GTGAGTGCCAGAGAATTTGAAAAGCTTTACTTTATTGCAAATGGTTTGGGGTGCAGAAAGCTCCAGAGTTCTCTTAATTGGCTTATCTGGGGGGGTTTCTTGGTTTCTTAGAGAACTGAAATAAATTAGAAAGAGCTTAACGTATCACTTTTTAGAAAGATACCCACTGCTGATGTATTCAGGCAGCTTTAATTTAACATGCTTCTCTTTTGTGTCAGTATTATCGTCAAAGCTGTGCACTTTTTTGCGATGTACTTACACTGTCTCTTGCACTGTGTGCAG
Seq C2 exon
GTCTCCCCGGCCAACCAGGGGCTCCAGGTATAACCCCACAGGCAGAAGAAATCACAGCCCCTGCAGGCTTACCAGGTCTGCCAGGGATTGATGGCGTCCCTGGCTTTGATGGAGATCCTGGATTCCAGGGCCCAGTTGGAAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:40
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=FE(54.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(19.7=24.0),PF0139113=Collagen=PU(51.7=62.0),PF0139113=Collagen=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTGAGCCTGGTCTCATGG
R:
GCTTTCCAACTGGGCCCTG
Band lengths:
236-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]