GgaINT0039356 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10282387-10282565:+
Coord C1 exon
chr8:10282387-10282440
Coord A exon
chr8:10282441-10282529
Coord C2 exon
chr8:10282530-10282565
Length
89 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
GCTTATACTCTTGTCCATAGGGT
3' ss Score
9.25
Exon sequences
Seq C1 exon
GGAATTTCTGGTCCTGCTGGTCCACTCGGACCCCCTGGTCCTCCTGGTTTACCT
Seq A exon
GTAAGTAATTTCACCCAGTTCTCCTGTTCTAAACACTCCCATGTTTTGTGGAATATATTCCAACTACATGCTTATACTCTTGTCCATAG
Seq C2 exon
GGTCCCCAAGGTCCAAAAGGTTCCAAAGGATCCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:60
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(21.4=83.3),PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAATTTCTGGTCCTGCTGGT
R:
TGGATCCTTTGGAACCTTTTGGA
Band lengths:
88-177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]