DreINT0048853 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28756082-28756261:-
Coord C1 exon
chr24:28756208-28756261
Coord A exon
chr24:28756127-28756207
Coord C2 exon
chr24:28756082-28756126
Length
81 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAAT
5' ss Score
1.19
3' ss Seq
AACTTCTTTCTTCTTTACAGGGA
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGTGAGACCGGCCCTGCTGGACCCCCGGGACCAACTGGAGAGGATGGACCAAGA
Seq A exon
GTAAATTTTTTTTTCATTCACCTTCTCTCAATATATTGGTTCACTCACTAGAAAAAAAAGTAACTTCTTTCTTCTTTACAG
Seq C2 exon
GGAGAAGATGGTGAGATCGGACCAAGAGGACTTGCTGGTGAGAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:19
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(16.7=77.8),PF0139113=Collagen=FE(23.9=100),PF0139113=Collagen=FE(20.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(18.3=86.7),PF0139113=Collagen=FE(17.1=100),PF0139113=Collagen=PU(15.5=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAGACCGGCCCTGCTG
R:
GCTCTCACCAGCAAGTCCTCT
Band lengths:
98-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]