DreINT0049428 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3094993-3095331:-
Coord C1 exon
chr12:3095266-3095331
Coord A exon
chr12:3095038-3095265
Coord C2 exon
chr12:3094993-3095037
Length
228 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TGGGGGTTTCTCTCTTGTAGGGC
3' ss Score
10.13
Exon sequences
Seq C1 exon
TCTTTCCTTTCCCAGATGGCTTATGGCAGTGAGAAGTCCAGCGGTCCTCCTCAACCCGGACCACCA
Seq A exon
GTAAGTCAGCTTCTCTGTTTGTCCTCATCCTCCAGTGGACAGAATAATCAGAAATGTGTTTGTACATCTCACGTATCATAACTCACTGCTATCGTGCATAAACATCAATGATGCTATTAGAATCGGTCATTTAACAATGTTTAATGTTGTTAAAGATTGGCTCATACTGACTTTTGCATTTACATTATTATCATATCTACATCTAACATGGGGGTTTCTCTCTTGTAG
Seq C2 exon
GGCCCCATGGGTCCCCGTGGCCCCCCAGGACCTGCAGGTTCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:6
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=PD(0.1=0.0),PF0139113=Collagen=PU(10.8=31.8)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]