DreINT0040075 @ danRer10
Intron Retention
Gene
ENSDARG00000026855 | cacna2d4a
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4a [Source:ZFIN;Acc:ZDB-GENE-041210-213]
Coordinates
chr4:20550488-20551245:-
Coord C1 exon
chr4:20551153-20551245
Coord A exon
chr4:20550619-20551152
Coord C2 exon
chr4:20550488-20550618
Length
534 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TTTTGATGGTTTCTTTGCAGAAA
3' ss Score
9.37
Exon sequences
Seq C1 exon
TATTGATGGGGGAGTGGAGACAGCGTTCCTGGGCACGCGCTCTGGCCTCATGAGGATGATCAGATATGCTGGCGTAGAGAAGCGTGTGGCGAA
Seq A exon
GTGAGTATACCTTTAATCAAGAGCTCCCGCTGTCTGCATCACGACTCAACTGCATAGGCTGCGTCTGCTCTGTCACAGGTTTCCTTGAGGCCACTCACTCCCACATATAACTTTCATCAGTAGGCACTCTAAAATACACTCAACACTGTAAGGTAAAGAGGAACAGGCGGTAATGCATAAAATACAGGCTGTATATATATGTTTTAGTTATAGGATAACCATATTTATGTACATCAAAGTAAGTAAGGCAATGACCACGCAACACATATAATTGGGTCAAAGACGAAAAGGGTATTTCTAAGCAAAAATGAACGACTTTAATACATTTTAAACATGATTTATTGTACATACGACATCCACTATTAACTTCACTAATGCCGTTAAGTGAAGCAATTGTTTATATATCAAAAATCTTGTCAGGCATAATTAGATCAAGAATCATTTGATGACATATTAAAAGACACCAAAATAGGACATCTCATCTTTGACCTATATATTAATGTTGGATGTTTTTTTTTGATGGTTTCTTTGCAG
Seq C2 exon
AAAATTCTTAACTGCATCAGATAAGGAGAATATTTTTACTCTAGACCATTTCCCTGTTTGGTATCGGCGTGCGGCAGAAAATCCAGCTGGCCGCTTTTTGTACTACGTTCCTACAGAGGACAACTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026855:ENSDART00000136069:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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:
TTGATGGGGGAGTGGAGACAG
R:
CTCCTGAGTTGTCCTCTGTAGG
Band lengths:
222-756
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]