DreINT0048922 @ danRer10
Intron Retention
Gene
ENSDARG00000009014 | col11a1b
Description
collagen, type XI, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-070912-607]
Coordinates
chr2:15793433-15793728:-
Coord C1 exon
chr2:15793675-15793728
Coord A exon
chr2:15793541-15793674
Coord C2 exon
chr2:15793433-15793540
Length
134 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
AAAACATTTTTGTTGTTCAGGGA
3' ss Score
6.77
Exon sequences
Seq C1 exon
GGTGAAGATGGTTTCCCTGGGTTCAAGGGAGACATGGGCCTCAAGGGTGACAAG
Seq A exon
GTAAACACCAAACACTTCCCAGAATTCAGTTTTGCTGCATTTAATTGCACTCATAGTCACTGATTAATCATTTGTCCAAGATAATTTAGCTTTTTCTATGACCTGTTTAATGTTAAAACATTTTTGTTGTTCAG
Seq C2 exon
GGAGAAGTCGGTGTGATCGGTCCCAGAGGAGAAGATGGACCTGAGGGGCCAAAGGGTAAATCAGGTCCAAGCGGAGAGGCCGGTCCAATGGGCACAGCAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009014:ENSDART00000049589:29
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(28.3=100),PF0139113=Collagen=PU(8.6=44.4)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=22.2),PF0139113=Collagen=FE(37.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAGATGGTTTCCCTGGG
R:
CTTCTCTCCTGCTGTGCCCAT
Band lengths:
162-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]