DreINT0038990 @ danRer10
Intron Retention
Gene
ENSDARG00000053462 | c3a.5
Description
complement component c3a, duplicate 5 [Source:ZFIN;Acc:ZDB-GENE-090311-30]
Coordinates
chr1:55450061-55451576:-
Coord C1 exon
chr1:55451489-55451576
Coord A exon
chr1:55450164-55451488
Coord C2 exon
chr1:55450061-55450163
Length
1325 bp
Sequences
Splice sites
5' ss Seq
CAAGTACAA
5' ss Score
-1.09
3' ss Seq
CAAATATTTTCTTTTGTCAGGTA
3' ss Score
7.93
Exon sequences
Seq C1 exon
TGCTGCCCAGCTTTGAAGTCAACTTGCGTCCAAGCAAACCTTTCTTCTATGTGAACCAAGAATCTCTGACTGTGGACATATCAGCCAA
Seq A exon
GTACAACTCACCATCACTGCTTTTCTTTTGTCCTTTTTTTTCGTTTGTCCGTCCTTTCATTCACCAGCCTATCAGTCCGTTCATCCTTCCTCTCGTTCATTTGTCAGTCCTTCCTTTCAATTGTCCTTTTGTTTGTTTGTTTTTTTATTCCTTTTTCCTTCCTTTCATTCTTTTGTCCTTCCTTTGTCCTTTCTTCCTGTCGCTTGTCCTTTCTTCCCTTTATAAATTCTTCCTTTCGTTCCTTTGTCCTTCCTTCCTTTTCAATCATCGTACCTTCCTTTTGTTTGTCCGTCCTTGCTTTGTTCGTTCTTTCTTTTGTTCATTAGTCCTTTTTGTTAGTTAGTTCATCCTTCCTTTCGTTCGTTTGTCCTTTTTGCTTGTTTGTCCTTAATTTTCTTAATTTGTCCTTCCTTTCGTTTGTTTGTCCTTTCTTCCTTTGTCCTTCCTTCCTTTCGTTTGTTCGTCCTTCCTTTCGTTTGTTCGTCCTTCCTTTTGTTCCTTTGTCCTTCCTTCCTTTTCAATCGTCGTTCCTTCCTTCCTTTTGTCCGTCCTTCCTTTTGTTCCTTTGTTCTTCCTTTCATTTGCTTGTTTGTCCTTTCATTCATTCATCCTTCCTTTTGTTCCTTTGTCCTTTCTTTCTTACTTACTTTCGTTCATCCCTTCCTTTGTTCCTTTGTCCTTCCTTCCTTTTCAATCGTTGTTCCTTCCTTCCTTTTGTCCATCCTTGCTTTTGTTTGTCCTTCCTTTCGTTTGTTTGTCCTTCCTTTTGTTCCTTTGTTCTTTCTTTCATTTGTTCGTTCGTCCTTTCATTCATTCATCCCTCCTTCCTTTTGTTCCTTTGTCCTTTCTTTCTTACTGTCGTTCATCCTTCCTTTTGTTCCTTTGTCCTTTCTTTCTTTCATTCATGCTTTCCTTCCTTGTTTTAGTTTGTTCATTTATTACTAATTATTTTAGTTTAGTTTGTATGTTTTTTTGTTAGTTTGTTCTTTGTTTCTTATCTGTTTTATTTTTCTCTTTTTGTTTTTTATTTTTCTTTGTTTTATTCTTTCATTTGTTTTTATCTTTGCTTAGTAGTTGATCTCTTGTTTTTTCATTAGTTTTTTTGTTTGTTATTTTTTATTTCCTTTTTTACTTTATGTATGTTCCTTTTTTGTTTATTCTTCTGTTTTTCTTCAATTTTTATCTCTTTAATATTGTTGTTTTTTCATCTGTTTCTTCTTTCTTAATTTATTTCTTTTTTTTTTACCTACTGTAGAACGAAATAATTTCTGTGCCTGTTATCATTGTAGATCTATTGCACATCCTCAAATATTTTCTTTTGTCAG
Seq C2 exon
GTATTTGTTTGGTAATAAGGTGCGAGGAAGTGCATTTGTGGTGTTTGGATTGGTGGACGGTGAGAAGAAGATCAGCATGGCGGCTTCACTGCAGAGAGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000053462:ENSDART00000133079:6
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:
NO
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:
TGCCCAGCTTTGAAGTCAACT
R:
GAACTCTCTGCAGTGAAGCCG
Band lengths:
186-1511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]