DreINT0048999 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7271109-7271531:-
Coord C1 exon
chr19:7271334-7271531
Coord A exon
chr19:7271163-7271333
Coord C2 exon
chr19:7271109-7271162
Length
171 bp
Sequences
Splice sites
5' ss Seq
CCAGTAATA
5' ss Score
-2.56
3' ss Seq
ATCTGACTCTGTTTTCTTAGGGT
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGTCCCTCTGGTGAGACTGGTCAGATGGGTGAGCGTGGCCACCCTGGACCTCCAGGACCACCTGGTGAGCAAGGCCTTTCTGGCTCCTCTGGTAAAGAAGGAACCAAAGGAGATCCCGGTCCTCCTGGTGGCCCCGGTAAAGATGGACCCCCTGGACTTAGAGGATTCCCAGGAGAGAGAGGACTACCAGGAACTCCA
Seq A exon
GTAATAAGACCTGCTGATTCTGCTCTGTGAATGATATAATGTTAAACTTTAACAATTGTTAAACTAAAATTTATAACTGTTTTACTGATTTATACCTGATTTACACCAATTTATAACTATGCCTAAATGTTTTTTATACCCCATAACTATAATCTGACTCTGTTTTCTTAG
Seq C2 exon
GGTTCTGGAGGACTGAAAGGAAATGAAGGCCCTGCTGGACCACCTGGTCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:39
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(12.0=15.2),PF0139113=Collagen=FE(66.3=100),PF0139113=Collagen=PU(48.6=53.0)
A:
NA
C2:
PF0139113=Collagen=PD(1.0=5.6),PF0139113=Collagen=FE(23.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCTCTGGTGAGACTGGTC
R:
CCAGGTGGTCCAGCAGGG
Band lengths:
244-415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]