DreINT0049398 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3086739-3087002:-
Coord C1 exon
chr12:3086949-3087002
Coord A exon
chr12:3086838-3086948
Coord C2 exon
chr12:3086739-3086837
Length
111 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGA
5' ss Score
4.08
3' ss Seq
CCTGAATGTCTAACTCACAGGGT
3' ss Score
5.46
Exon sequences
Seq C1 exon
GGTATGACTGGTGCCCCTGGAAGCCCTGGACCTGATGGCAAAGCTGGACCTTCT
Seq A exon
GTAAGATTTTATTTTTGTCATTCATTGTGTAGTTTTTGTATGCAGTGTAGAAATGATATCAGATATAATCTTGTGTTTAAATGAATGTTTGCCTGAATGTCTAACTCACAG
Seq C2 exon
GGTGCACCTGGACAAGATGGTCGCCCTGGACCCCCAGGACCTGCCGGATCTCGTGGTGCTCCTGGAGTTATGGGATTCCCTGGGCCCAAAGGAACCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:24
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(41.0=97.0)
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:
TATGACTGGTGCCCCTGGAAG
R:
TTCCTTTGGGCCCAGGGAATC
Band lengths:
146-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]