DreINT0040131 @ danRer10
Intron Retention
Gene
ENSDARG00000002167 | cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:ZFIN;Acc:ZDB-GENE-040718-399]
Coordinates
chr3:16041338-16041995:-
Coord C1 exon
chr3:16041873-16041995
Coord A exon
chr3:16041475-16041872
Coord C2 exon
chr3:16041338-16041474
Length
398 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
TGGGTGTTTTCTGTTAACAGAAG
3' ss Score
7.32
Exon sequences
Seq C1 exon
ACCAAGCCTGTAGCGTTTGCAGTGAGGACTAACGTTGGCTATAACCCAGGCCCTAATGATGATGTGCCTGTTCAGGGCATGGCCATCTCTTTCGAACCCAAAGACTTCCTGCACATCAAAGAG
Seq A exon
GTCAGACAAGCACACTTACCTTACCTTAAAATGTGTTGAAAGCATTTTGGCTTTCACCTGTAAAATGACAGATGTTCCTGAAGTAATAGTTTAAGAAATCACACTGTTATGACAGCAAAAAAAATAAGTTTGTGATCAATCTTCATTTTATTGCCCAATCAGATGATGTGCTGCACCTCTTAAGTGTTTAATTTGGCTTACATTTCTTTGAAAGGGGGTGTTTTTTTAAACTAATTGGCTACATTTTCAAATATCTTTAATTTGCTTAGTTTGTTTCTGTAATCTGATGTATGATTGAAGCCTTCTTTAATATATTTATAGGTATATTTTCTTATATTGATGGTAAATGTATCTGCTGCTTAAACGTGATTCAAAGGCTGGGTGTTTTCTGTTAACAG
Seq C2 exon
AAGTATAATAATGACTGGTGGATCGGGCGTTTGGTGAAGGAGGGATGTGAGGTGGGCTTTATCCCCAGTCCAGTGAAGCTCGAGAGCACTCGGCAGTTACAAGAACAGAGAATGAGACAGAACCGCCTTAGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002167:ENSDART00000111707:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.561 A=NA C2=0.435
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)
A:
NA
C2:
PF0001823=SH3_1=PD(51.2=47.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTAGCGTTTGCAGTGAGG
R:
CTGGAACTAAGGCGGTTCTGT
Band lengths:
254-652
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]