DreINT0049430 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3094669-3094897:-
Coord C1 exon
chr12:3094844-3094897
Coord A exon
chr12:3094723-3094843
Coord C2 exon
chr12:3094669-3094722
Length
121 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TATTAATAACCTGTCTGCAGGGT
3' ss Score
6.46
Exon sequences
Seq C1 exon
GGCCCTCAGGGATTCACTGGCCCCCCAGGCGAGCCTGGTGAGCCTGGTGCTCCT
Seq A exon
GTAAGTACCTTGCATTTACTTTATTCGTTCTCAGTGTTTCTGTGTGACATAATATAGCCTGCTTTAGATTTTACAGAGCATACATATTTGCTGAATATTATTATTAATAACCTGTCTGCAG
Seq C2 exon
GGTCCAATGGGTTCTCGTGGTCCTCCCGGCCCTCCTGGAAAGAACGGAGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:8
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(26.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(26.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGGATTCACTGGCCCC
R:
TCTCCGTTCTTTCCAGGAGGG
Band lengths:
100-221
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]