GgaINT0039357 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10282530-10282727:+
Coord C1 exon
chr8:10282530-10282565
Coord A exon
chr8:10282566-10282673
Coord C2 exon
chr8:10282674-10282727
Length
108 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TTTCTTTCATTACTTTATAGGGT
3' ss Score
9.54
Exon sequences
Seq C1 exon
GGTCCCCAAGGTCCAAAAGGTTCCAAAGGATCCAGT
Seq A exon
GTGAGTAATTCTCCATATTTTCTGGTTTTGTGCTTCATTTCTGTGTGTACATTATTTTTTAATATAAAGTAGTATGGTCAATAACACATTTCTTTCATTACTTTATAG
Seq C2 exon
GGTCCTGCTGGCCAAAAGGGTGACAGTGGTTTACCTGGCCCACCTGGTCCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:61
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=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:
GTCCCCAAGGTCCAAAAGGTT
R:
CCAGGTGGGCCAGGTAAAC
Band lengths:
82-190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]