DreINT0040065 @ danRer10
Intron Retention
Gene
ENSDARG00000026855 | cacna2d4a
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4a [Source:ZFIN;Acc:ZDB-GENE-041210-213]
Coordinates
chr4:20553131-20553469:-
Coord C1 exon
chr4:20553389-20553469
Coord A exon
chr4:20553206-20553388
Coord C2 exon
chr4:20553131-20553205
Length
183 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCT
5' ss Score
5.39
3' ss Seq
TTTTTCCATTCTCATTTCAGCTG
3' ss Score
10.59
Exon sequences
Seq C1 exon
CTCTCTCATGGCATCCTCCTCGGTGTGGTTGGCACTGATGTTCCCTTGAAGGAGCTCATGAGATTGGCTCCTCGATACAAG
Seq A exon
GTGCCTTAATAATATCATCAGTTCTCTGTTGATCACATCTAACTCTTTTCCATTCACAGAACAGACTGTGTCCATGGAGATTATTGCATACAGAGTGACTGATTGTTTAGACACCAGACTGAATAATAAATATGTGATTTTCCTGAATGATTTATTCTGATTTTTTTTCCATTCTCATTTCAG
Seq C2 exon
CTGGGGGTTCACGGCTATGCATTCTTAAACACTAATAATGGTTATATACTCTCTCATCCTGACCTTCGACCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026855:ENSDART00000136069:14
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:
PF0274313=Cache_1=FE(30.3=100)
A:
NA
C2:
PF0274313=Cache_1=FE(28.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTCATGGCATCCTCCTCG
R:
AGAGGTCGAAGGTCAGGATGA
Band lengths:
154-337
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]