GgaINT0045675 @ galGal4
Intron Retention
Gene
ENSGALG00000012511 | CACNB4
Description
voltage-dependent L-type calcium channel subunit beta-4 isoform c [Source:RefSeq peptide;Acc:NP_989675]
Coordinates
chr7:34852556-34853140:-
Coord C1 exon
chr7:34853021-34853140
Coord A exon
chr7:34852679-34853020
Coord C2 exon
chr7:34852556-34852678
Length
342 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCTT
5' ss Score
4.72
3' ss Seq
ATGCCTGTTTCTGTTCGTAGTCC
3' ss Score
8.17
Exon sequences
Seq C1 exon
GGCTCAGCAGATTCGTACACAAGCAGACCCTCAGACTCTGATGTGTCTTTGGAAGAGGACAGGGAAGCGATCCGCCAGGAGAGAGAGCAGCAAGCGGCGATACAGCTCGAAAGGGCAAAG
Seq A exon
GTGCTTTCTTTTAAACTGTGATAGCGGCTGCTTATGGGGCAGTCACCGTCTGCCTGCTGTTAAGATTCGTACCGCTCATTTATAGTGGTGATGGCATGCTGACAGTCAAGTGAGATTTCCTGCAAGCCAAACTGGGGGGGGGGAATGTAGTGTAAATATTCTTGAATAAGTGGGGATCTTCTTTAGTGAACTGGACTCTCTTGGCTTGTGTGAAACTATTAGGTCTGAATTTTGATGTATTTGGCAAATACCCTCCACTAAATTTTTGGCAATTTGATACAGAAAATTAATTCCTGATGCAGGAAAGTTTCCGCTGTTTATGATGCCTGTTTCTGTTCGTAG
Seq C2 exon
TCCAAACCAGTAGCGTTTGCTGTTAAGACCAATGTGAGTTACTGTGGAGCTCTGGATGAAGATGTCCCTGTCCCAAGCACTGCCATCTCTTTTGATGCGAAGGACTTCCTACACATTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012511:ENSGALT00000020437:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.875 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PU(92.9=97.5)
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCAGCAGATTCGTACACA
R:
TAATGTGTAGGAAGTCCTTCGC
Band lengths:
238-580
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]