GgaINT0097886 @ galGal4
Intron Retention
Gene
ENSGALG00000008591 | CACNB2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:HGNC Symbol;Acc:HGNC:1402]
Coordinates
chr2:19072486-19074365:-
Coord C1 exon
chr2:19073457-19074365
Coord A exon
chr2:19072606-19073456
Coord C2 exon
chr2:19072486-19072605
Length
851 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGC
5' ss Score
4.52
3' ss Seq
TTTTCCTTCCCTTTGTGCAGGGC
3' ss Score
10.6
Exon sequences
Seq C1 exon
AAGCGCTATGTTACAACATCCTTGCTTTTCTCATCTGCCCATGTCAGACGAATATGAGCAGTGATGAGGGGGTTAATTCCTGCTCAACAGGCACGTTTCTGTATTCAGGGCTGTGCGTAGCATGGAGCAGGGCTGGCAGCAGACGTGTGCGACAGCAGTGAGATGCTGTACCAGCCTGTCCAGTTTTCCCTCGCGTTTTCCAGCTGTTTACCCTTGAGATGTAAAATGGCAATTTGGCATAGGCTACCGGCACGGTGTGATGTGAGCATCTGCGTAAAAGGCTGCACGGATGGAGCATGCCCAGTGCTCTGAGCAGCCCGTTACCCCACCCCCAGCCAATCTAGGAGGAGATGAAATGAACTTTGCACTTGCAAATGTCACTGAATGCATTTTGCACAGGATTTTAAAAGGTTCTCTTACAAGCACTATTTTTAACAGCCAAATCCGCCCCCCCAAATGAAAAAAGCCCTAAGTATTTTTCTGTGATCGACCTCAGTTATTATCAATTGAAGCATCTCTCACAACATTTACCTGAAGTCTGGCGTGTTTTACCTTTTTATCATTCAAACTGAGCTTTTTTTGGTGGTGGTGTGGATATTTTCTTTTTTTTTCTGATTTTTTTTTTTAACTGGCATGAGAATATTTGTGAATATAATTGCACTAGAATACTTGGAAACAGTGAGGCTGCAAGCTTGAAAGGCAGAGGGAAGAGAAGAAAGGCTCTCGCAGCAGAGCATGGATAGGAAAGGAGCGGTGATTCTGCGGTGCTCAGCGTGCACATGTTGTGTGAGATCAGTGCCGGGCGCTGCAGCTGCGGACAATAACTGAGCTGTCTGGCTAATGAAGGCCACCTGGATCAGGCTTCTGAAAAGAGCCAAAGGAGGACGTCTGAAGAATTCTGATATCTGT
Seq A exon
GTAAGCCCTGTCTTTTCATTATTGGCGTATATTCTATGTGTTGCAGAGAGGGAAGGAGGAAAAAAAAAAAAGAAAAAAAAACACGGTGTGGAGAGGACAGTTGTTTTCATTCTAATTGAATTAGCAGAACTCTGTTTTGTATGCAGGGAGATGCAGAGGGAAATCAGAGCTGTCATTATTTATAGAGCTGTTCTGGCATTGGGACTGCTTCCATTGTGGCAGTTTGTGGACCTGCGTTGAGTCCAGACAGATTTTATTAGCAAGAAGTTGATTTGTGGTCATTTACATGTTTTGCTGAGGGGTAGGAGATGGATACGAGCCATTTGCAGTTCTAATGGGGAAAGTGTGTCAGGTAAAGAGGTTGCCCTAAAATAAATGCATAGCAGAAATTAAATCTGCAATCAGGAGTGTTGTGTCACGGTAATTATTGATGGTGAAGTAGCATTTTGATTGTAAAAATGTGTTTCCTTGTTAATAATGTCACTGCTTAGAGTTCTCTTTTTTATGGAGCCATCCTTGAAGCTGCTGTGTGTCCTTCAGCCCTGCACTGCACCACTGCTGTAACTCTACAGAGCGACTGGCACAGTTTACTAAAATGCATACAGATCAGCACACAGGCATAGTGCAGGAAATGCAACACAAGGGAAGACACCTGTACTTTGGAAGTTCTCTGGAAGAAAATGTCTTTTTAGATAAATTTCACTAAGCGTCCTTCCCTTTTTGGCAGTTATTCTCTTTTCAGGGATACAGATGTAAGAGGAAGGACAAGCTCTATAACCACTTCTGCTTTTTTTTTTTTTTTTTGGATTCTAGAACAACTTGTGATACTATTTTTCCTTCCCTTTGTGCAG
Seq C2 exon
GGCTCGGCGGACTCCTACACCAGCCGTCCATCCGACTCCGATGTATCTCTGGAAGAAGACAGGGAAGCAGTGCGGAGAGAGGCAGAGCGACAGGCCCAGGCACAGTTGGAAAAAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008591:ENSGALT00000013988:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.750
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PU(92.9=97.5)
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:
AGTGAGGCTGCAAGCTTGAAA
R:
GCTTTTTCCAACTGTGCCTGG
Band lengths:
348-1199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]