DreINT0040067 @ danRer10
Intron Retention
Gene
ENSDARG00000026855 | cacna2d4a
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4a [Source:ZFIN;Acc:ZDB-GENE-041210-213]
Coordinates
chr4:20552394-20552657:-
Coord C1 exon
chr4:20552571-20552657
Coord A exon
chr4:20552466-20552570
Coord C2 exon
chr4:20552394-20552465
Length
105 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
TGTGTGTGGTGATCCTTTAGCTG
3' ss Score
6.13
Exon sequences
Seq C1 exon
TATAAAGATGGCAAGAAGCTGAAGCCAAAGCCGAACTATAACAGTGTGGATTTATCAGAGGTGGAGTGGGAGGATACAGAAGATGCA
Seq A exon
GTAAGTGGAATATTAATAAACACTCACTCACACACATACACGCACGTACATCACACCATTTTTAGATCAATTGCTTCAAGGTGTTTGTGTGTGGTGATCCTTTAG
Seq C2 exon
CTGAGAACGGCGATGGTAAAAGGGGAAACTGGGACAATCTCTCTGGACGTCAGAGCAACAGTAGAAAAAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026855:ENSDART00000136069:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0274313=Cache_1=PD(7.9=23.3)
A:
NA
C2:
NO
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:
AGATGGCAAGAAGCTGAAGCC
R:
TCCTTTTTCTACTGTTGCTCTGACG
Band lengths:
154-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]