DreINT0049391 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3089001-3089261:-
Coord C1 exon
chr12:3089217-3089261
Coord A exon
chr12:3089100-3089216
Coord C2 exon
chr12:3089001-3089099
Length
117 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
GTTTGCATGGCCATTTTAAGGGT
3' ss Score
4.85
Exon sequences
Seq C1 exon
GGAGGACCTGGTTCTGATGGCACTCCTGGTGGCAAAGGATCTCCT
Seq A exon
GTAAGTATTCTTATATTTTATTTATATAACTTTACTTGGTATTTATTAATTAAAATTCATTGTATTAATCCACCCAATTCTGTATGTAATTAAACTGGTTTGCATGGCCATTTTAAG
Seq C2 exon
GGTGCTGCTGGTATTGCTGGTGCTCCTGGTTTCCCTGGTGCTCGTGGACCACCAGGACCCGCTGGACCTAATGGAGCTCCAGGCCCCAAAGGAAACAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:18
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(17.3=100),PF0139113=Collagen=FE(19.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.3=42.4),PF0139113=Collagen=FE(44.4=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:
GACCTGGTTCTGATGGCACTC
R:
ATTGTTTCCTTTGGGGCCTGG
Band lengths:
140-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]