DreINT0048914 @ danRer10
Intron Retention
Gene
ENSDARG00000009014 | col11a1b
Description
collagen, type XI, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-070912-607]
Coordinates
chr2:15807403-15807587:-
Coord C1 exon
chr2:15807534-15807587
Coord A exon
chr2:15807448-15807533
Coord C2 exon
chr2:15807403-15807447
Length
86 bp
Sequences
Splice sites
5' ss Seq
CGTGTATGT
5' ss Score
5.08
3' ss Seq
TTGTGTTTTCACACATGCAGGGA
3' ss Score
8.02
Exon sequences
Seq C1 exon
GGTCCAAGAGGTCTGCTGGGCCCCAGAGGATCTCCTGGTACTGCTGGACAGCGT
Seq A exon
GTATGTACTACCAGACTTTTTCTTAGTCACAAATATTCTAATATCATGAAACTGACAGCCAGACACTTGTGTTTTCACACATGCAG
Seq C2 exon
GGACTGACTGGTTTGGATGGACCACCTGGCCCTAAAGGAAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009014:ENSDART00000049589:21
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(19.5=100),PF0139113=Collagen=PU(16.1=77.8)
A:
NA
C2:
PF0139113=Collagen=FE(16.1=100),PF0139113=Collagen=FE(16.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCAAGAGGTCTGCTGGG
R:
GTTTCCTTTAGGGCCAGGTGG
Band lengths:
96-182
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]