DreINT0048895 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28705991-28706220:-
Coord C1 exon
chr24:28706167-28706220
Coord A exon
chr24:28706045-28706166
Coord C2 exon
chr24:28705991-28706044
Length
122 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
GTTGGTTGTGTGATATTTAGGGA
3' ss Score
4.99
Exon sequences
Seq C1 exon
GGTGAACAAGGACTTCCTGGTGCTCCTGGACAAGATGGTCCACCTGGACCAATG
Seq A exon
GTAAGAGAAAAGATCATGTTTCTCTTATTCTTTCTTTCTGTCAACACTTCATCTTCTCTCTTGCTCTCTCAGTTGTACATGGGCACAAATTGAATTGTCCTTGTTGGTTGTGTGATATTTAG
Seq C2 exon
GGACCTCCTGGTCTGCCTGGCCTTAAAGGAGACCCTGGCTCTAAGGGTGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:57
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(20.7=100),PF0139113=Collagen=PU(7.0=27.8)
A:
NA
C2:
PF0139113=Collagen=FE(20.7=100),PF0139113=Collagen=FE(23.9=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:
AGGACTTCCTGGTGCTCCTG
R:
CTTCTCACCCTTAGAGCCAGG
Band lengths:
100-222
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]