DreINT0038986 @ danRer10
Intron Retention
Gene
ENSDARG00000053462 | c3a.5
Description
complement component c3a, duplicate 5 [Source:ZFIN;Acc:ZDB-GENE-090311-30]
Coordinates
chr1:55452119-55452848:-
Coord C1 exon
chr1:55452680-55452848
Coord A exon
chr1:55452193-55452679
Coord C2 exon
chr1:55452119-55452192
Length
487 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGA
5' ss Score
7.63
3' ss Seq
TAACTTGACGTATTTTGCAGTGA
3' ss Score
6.06
Exon sequences
Seq C1 exon
ATCCGTGATGATCTGAACTTCTTCTCTGATGACCCTCTGGAGAAGCAGTATGTGTATCTGCAAGCTATTTTCCCGACTCACACTCTGGAGAAAGTGGTCTTGCTGTCGTTCCAGTCTGGATATTTGTTTGCACAGACTGACAAGCCCATCTACACGCCTTCTAGCACGG
Seq A exon
GTATGAGCTGGTCAAACTTTTCAAAAGAGTGACGAGTTTTCTGTGACGCGCTCCTGATATTGTTTACCGCTACTCTGAATATTCAGTGTGGCTTAGTAATAAGTGAAATTCCTGCTCGCCGCCCGGCCAACCACTACATACACTTCTAACTGGCGAATGAACTGGGTTGACTGCTGTTGTGTCGCGGTGGGCGCGCTCGTGATTTCAAGAGGCGTGGCTTTGAAACACAGTCCCTCCCTGCTGTCCAAAGCTAATATGCTATCCGATTAGCATTTTGGCAGATCAGCTACTGCACTTTTAATTTTTTGCATTAAATTCAATGAAAGCCAGGTGGTTTGAGAGTGTATTATAGAAAAGTGTTATTTTGTAAATTGTATATGTATTTTTTCCATGAAATGGCTATTGATACGGTAATAAGCTCTAAACTCGCTTAAAATACATGCATTGTATTGTGCATGAAACAAAGCTAACTTGACGTATTTTGCAG
Seq C2 exon
TGAATTACAGGATCTTCTCTCTAACCCCGGATCATCTTCCGTTTGATGGAGCTTCGATCTCTGTCGATATCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000053462:ENSDART00000133079:2
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=PU(15.8=26.3)
A:
NA
C2:
PF0183514=A2M_N=FE(26.3=100)
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:
ATCCGTGATGATCTGAACTTCTTCT
R:
TATCGACAGAGATCGAAGCTCCA
Band lengths:
238-725
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]