DreINT0049401 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3084568-3084770:-
Coord C1 exon
chr12:3084717-3084770
Coord A exon
chr12:3084622-3084716
Coord C2 exon
chr12:3084568-3084621
Length
95 bp
Sequences
Splice sites
5' ss Seq
GCTGTACGT
5' ss Score
5.68
3' ss Seq
CCTGGCCTGTCGTCTCATAGGGA
3' ss Score
10.08
Exon sequences
Seq C1 exon
GGAGCTCCTGGTAAGGATGGTGATATCGGTAGTCCTGGTGCTCCTGGACCTGCT
Seq A exon
GTACGTCTGCTAAAACCTTTAAAAGTTTGATGTATTACAAATCAATTATTTCAGTGTGAACTGTTCTGACTTTGCCCTGGCCTGTCGTCTCATAG
Seq C2 exon
GGACCTGCTGGAGAGAAAGGAGAACAGGGATCTGCTGGTCCTTCTGGATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:27
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(21.8=100),PF0139113=Collagen=PU(21.8=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=44.4),PF0139113=Collagen=FE(21.8=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:
CTGGTAAGGATGGTGATATCGGT
R:
TCCAGAAGGACCAGCAGATCC
Band lengths:
95-190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]