DreINT0040185 @ danRer10
Intron Retention
Gene
ENSDARG00000009738 | cacnb4a
Description
calcium channel, voltage-dependent, beta 4a subunit [Source:ZFIN;Acc:ZDB-GENE-080320-2]
Coordinates
chr9:38301574-38301935:+
Coord C1 exon
chr9:38301574-38301690
Coord A exon
chr9:38301691-38301812
Coord C2 exon
chr9:38301813-38301935
Length
122 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGA
5' ss Score
4.3
3' ss Seq
GTGCTTTAAATCGGTTTCAGGCC
3' ss Score
7.16
Exon sequences
Seq C1 exon
GGCTCCGCCGATTCCTACACTAGCAGACCATCTGACTCGGATGTCTCTTTGGATGAGGAGCAAGGCGGCCGGCAGGAGAAAGAACAGCAGGCCACCGTTCAACTGGAGAGGGCAAAG
Seq A exon
GTCTGACTGTTTAAACCAGAGCCATTACACATGCATTATCTGCTTGCTCAAAGTCCATATTTGGGGTAATTGAAACCACACTTTAATTCTGTTTTTGGATATGTGCTTTAAATCGGTTTCAG
Seq C2 exon
GCCAAAGCGGTGGCCTTTGCTGTGAGGACAAACGTCAGCTACTGCGGTGCCCTGGATGAAGATGTTCCTGTCGCTGGCACAGCCATTTCTTTTGATGCTAAAGATTTTCTTCACATCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009738:ENSDART00000123749:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.744 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PU(92.7=97.4)
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(42.9=43.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCGATTCCTACACTAGCAG
R:
TCCTTGATGTGAAGAAAATCTTTAGC
Band lengths:
234-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]