DreINT0050116 @ danRer10
Intron Retention
Gene
ENSDARG00000101816 | col5a3b
Description
collagen, type V, alpha 3b [Source:ZFIN;Acc:ZDB-GENE-110728-4]
Coordinates
chr1:58562362-58562586:-
Coord C1 exon
chr1:58562497-58562586
Coord A exon
chr1:58562416-58562496
Coord C2 exon
chr1:58562362-58562415
Length
81 bp
Sequences
Splice sites
5' ss Seq
ATGGTAACC
5' ss Score
5.31
3' ss Seq
ACCTGTGTTCTCTCGTGTAGGGG
3' ss Score
11.13
Exon sequences
Seq C1 exon
GGGGATCCTGGAGGTCAAGGCACTTCCGGGAAGAACGGTCCCACAGGTCTGAAGGGCTTCCGTGGCAGTCGTGGAGCACCGGGTGCCATG
Seq A exon
GTAACCTAAGAACACCTTCTGTCCTCTGTCAGGCTTTCTGATTGGCCAGGTTTGTCATGTGACCTGTGTTCTCTCGTGTAG
Seq C2 exon
GGGCCAGTTGGATTAAAGGGAGGGACGGGGCCAATCGGGCCCCCAGGACCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101816:ENSDART00000170580:38
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(35.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.0=100),PF0139113=Collagen=PU(15.7=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCTGGAGGTCAAGGCACTT
R:
GTCCTGGGGGCCCGATTG
Band lengths:
135-216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]