GgaINT0097889 @ galGal4
Intron Retention
Gene
ENSGALG00000008591 | CACNB2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:HGNC Symbol;Acc:HGNC:1402]
Coordinates
chr2:19029262-19031142:-
Coord C1 exon
chr2:19031006-19031142
Coord A exon
chr2:19029339-19031005
Coord C2 exon
chr2:19029262-19029338
Length
1667 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
AATTTGTTGCTTTACTGCAGTAA
3' ss Score
5.17
Exon sequences
Seq C1 exon
AAATTTAACAATGACTGGTGGATAGGACGGTTGGTAAAAGAAGGCTGTGAAATAGGATTCATACCAAGCCCAGTCAAACTAGAAAACATGAGGCTGCAGCATGAACAGAAGGCAAAGCAAGGGAAATTCTACTCCAG
Seq A exon
GTAACAAGAAGAAATCATTAAAAATAGTAGTGCTGCCTCTAACGGTTAATTTGGAAATTAATGTTGTGCATGCTATACATCTCTTTAATTCTTATGATTGACAGTTAAAGAATGTTGAATCAATGAAAAATATATATTTATTTATACAGTTAATAATGTCATTGCAATTACAGAGGGAGTGCACATGCTTAGACTGGTGGTCTGTGATGATCTATGATGGAGTATGATTTACTGCGCGCAAGCACAGAAATCAGTCCCTCTAAATGTTACACTATTTGTTACTTTTTTCACAGTGTTACATTCACTAAACACCTTTAAAGTTGATTTCAGAAATTAAAGAAAATATTAAGATGAATTTGCTCATAAGCTTTAGCTCTTAGGAAAAACATTTGGGTTTGTCAACTACATTTCAGTTGAATACAGCTGTTAAAATACTGCTTTTATGATGGAAGTTTCTGACTGTAGCCATCATTATATAGAAACAAAAATTCAATATATAAACATTTCGTCCAATACTGCAAGACAGTAATAATATATTCTTTAGTATGGAATTCTTAATGCAGTAGTTTTCCATCAAATAGTAACACATGTAGAAACAAATGCCATTTGTTTCTCCTTGGGTGTATAGGAAATAGAAATATTTGTAGTATGTCTAAATGGCAGGGAGTTGGAAGTGGGGGAACAGCTGGGAAACATTTAGGAAGTCAGAAAGGCTTTCTATTCCAATGGCGAGGGCAGCAGTATTTGAAGAGCGTGTCTACATGAGCAGGGGACCAGGATGCTGCACTGCTCATCCGTGTTCACTGGCTGTGAAATGCTTTTCCTATAAGTTCCCTATCCTTAGCAGGAGGAAGTCAGGCTCCTTGCTCTGCTCCTACCATTTCTGCTATAGCCAAGTCTGACCCAATGTTTTGTTCTTTTCCCAGATTGTAAAAACTTTAATTCTCCAGAACTTCATACTGGAGATAACGTTGCTGTACACTACAAATGAATTTACTTAGTGATTATTAATATTTTAAGATGGGGAAAGTGTCAACTAGTACTGTTACATTAGTTTTTTAAAAAGGATATAGCATTTCTTACATTCATTTTAGCGTTTTTCTCATTAGAGTAATTGAAATAAACTTATTAAAAATATTGTTTCATATGCACAGCTTGAATAGGCTTTCACAAAGCAGAACTTGACTTAATCTTAAACTGTTTGTAACATACTTTGACAGGCTTATTTTTTGTAAGTTTATACCAAAATAACAAATAAACTTTTACATAATTTGAAAATATTTTAGACAAGCACACTATTAGTTTCACTTGGGTATTCTTAATAACTATTCTGTTAAAGGAAATATGTATACTCACTGATATGAGAATTAATCATAGTAATAAACAATATTATTAGTAATGATATTAATGCCATTAACAGCTAGATCACAATAAGGACATAAAGGCATATGCAACAGAATGAACCTGCAGAGCAAGGAGCATGACTGGTTTTTGCACATCCTCAGTGTTCAAAGTGTACATTCATTTTGTGTAAAATATATATTTCATGCTACTGTCAGAAATACTGTTTGTTCTCAGCTAGCAGCTAATTTAGAAAAAAATAAATAAGGTAGAATAAATACTCAAAAAGCTGTAAAACTACAAACTAATTTGTTGCTTTACTGCAG
Seq C2 exon
TAAATCAGGAGGAAACTCTTCATCCAGTCTGGGTGACATAGTTCCTAGCTCCAGAAAATCGACGCCTCCATCATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008591:ENSGALT00000013988:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.391 A=NA C2=0.852
Domain overlap (PFAM):
C1:
PF0001823=SH3_1=PD(51.2=47.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATTTAACAATGACTGGTGGATAGG
R:
CAGATGATGGAGGCGTCGATT
Band lengths:
214-1881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]