DreINT0040183 @ danRer10
Intron Retention
Gene
ENSDARG00000009738 | cacnb4a
Description
calcium channel, voltage-dependent, beta 4a subunit [Source:ZFIN;Acc:ZDB-GENE-080320-2]
Coordinates
chr9:38315038-38315869:+
Coord C1 exon
chr9:38315038-38315133
Coord A exon
chr9:38315134-38315683
Coord C2 exon
chr9:38315684-38315869
Length
550 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TTGTTCCTGCACCATTTCAGGAG
3' ss Score
7.7
Exon sequences
Seq C1 exon
GTATTACAACGGCTGATTAAATCAAGAGGAAAGTCTCAGAGCAAGCATTTAAATGTACAACTGGTGGCAGCAGACAAATTAGCTCAGTGCCCTCCA
Seq A exon
GTGAGTATCCAATATGTACACAATATATACAAAAATTGCAAATTTAAAACAGCTATTATGTATTTAAAAGCACAAGGAAATTTATATAATATTAGTAATGAAATAGTATACTAATATTTGTGTGATGGGAAAGAAGGGTTTTCATCAGAGATTACTCTAGTCTTCAGCGTCTTGTGATGCTCATTTTGTTCTCAGTTAACAGAATGTATTACTACCACTTATGTTGAAAATACTTGTGCAGCTTTCATGATGCTTTGATGCATCACAAGTTCAGAAGAACAGCATTGATTTAAAATACTGCAAATTATGTTAATCCATGGTTGCTAAATACAAGTAATAATTTCTTTCAAACTAAAATAAAATTCTAGACTCTCTACAAGCCTTTGGATGCTAATATAAAGCAGGACAATGTTACCCAAAAAATTCCATTACTGTTTGATTCAATAGTGAAAAGTGTAGTAAAAAGGAGGGATAAGGTTGGACGGAGGATGAGTTTAGGATGTGATGTATCACTAACTCGGATTGCATTGTTGTTCCTGCACCATTTCAG
Seq C2 exon
GAGATGTTTGACATAATTTTGGATGAGAATCAGCTGGAGGATGCGTGTGAACATCTATCTGAATATCTGGAGGCTTATTGGCGCGCAACACACACTTCCCTTAGCACTCCACTAAACCCTCTGCTGGGCCGCAATCTGGGCTCCACTGCACTCTCACCGTACCCCACAGCCATCTCTGGACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009738:ENSDART00000123749:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.323
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(17.1=100)
A:
NA
C2:
PF0062516=Guanylate_kin=PD(13.8=40.3)
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:
TACAACGGCTGATTAAATCAAGAGGA
R:
CTGTAGTCCAGAGATGGCTGTG
Band lengths:
278-828
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]