DreINT0038989 @ danRer10
Intron Retention
Gene
ENSDARG00000053462 | c3a.5
Description
complement component c3a, duplicate 5 [Source:ZFIN;Acc:ZDB-GENE-090311-30]
Coordinates
chr1:55451489-55451739:-
Coord C1 exon
chr1:55451657-55451739
Coord A exon
chr1:55451577-55451656
Coord C2 exon
chr1:55451489-55451576
Length
80 bp
Sequences
Splice sites
5' ss Seq
ACGGTGCGT
5' ss Score
10.25
3' ss Seq
GGATTGTTTTGTTCCTGTAGTGC
3' ss Score
6.27
Exon sequences
Seq C1 exon
TGCTGGGGTTTGGAAGTTGATTGCCAGATACACAAACACACCGCAGAAAAACTTCACCACTGAGTTTGAGGTTAAGGAGTACG
Seq A exon
GTGCGTTTCTGCCTTCTGGTTCTGTTAAAACTCTGTAAAATATTAAATATTAAATTTAGAGGATTGTTTTGTTCCTGTAG
Seq C2 exon
TGCTGCCCAGCTTTGAAGTCAACTTGCGTCCAAGCAAACCTTTCTTCTATGTGAACCAAGAATCTCTGACTGTGGACATATCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000053462:ENSDART00000133079:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0183514=A2M_N=PD(25.3=85.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGGGGTTTGGAAGTTGAT
R:
TGGCTGATATGTCCACAGTCAGA
Band lengths:
170-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]