GgaINT0120273 @ galGal4
Intron Retention
Gene
ENSGALG00000013007 | CACNA2D4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:HGNC Symbol;Acc:HGNC:20202]
Coordinates
chr1:61214396-61216185:-
Coord C1 exon
chr1:61216126-61216185
Coord A exon
chr1:61214559-61216125
Coord C2 exon
chr1:61214396-61214558
Length
1567 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTCATTGTCTTCATCAACAGTTT
3' ss Score
8.18
Exon sequences
Seq C1 exon
AGGTTGGTGGAAGCAGCAGAGGATGCAGATCTGAACCATGAGTACAACTCCTCACTGGAG
Seq A exon
GTGAGTTGGTCCCCCTCAGTGACAAAACATGGCACATATCCTCATAAGGACCAGGCAACAGGCTGACCTAGCAGCACCCTCCCACCTCTAGCACCTCATGCAGCACACCTGACCTTCTATCTAGGAGCCAGGCTAGTAGTATCCTTGTCCTCAGAACACTCAGCTTGTCTAGAAACCAGTATGACTCCTTGGGCAGATCCCAAGCCTAAGTAACACCTAGGGGATTAGTCCCTTTCTCACAGGGGTGAGAAAGATTTGGGAAGACATTGGGTTGTACGATGTTACAATGGAGGTTTTACCTTTATTGCATACCAACATTGTCATTATGTGACACATTAGTACAAATTAGCTGGTGCTTCCCGGTTTACTTACCTGGGAAATTAGCTAAACATTGATGTATGAGCAACAGGGAGGGTTCTGTTGCAAAGGTCGTGATGTTGCTAATACTCATAGCAAACTATTAATTCCAGTGAGCGGAGTTTCTCACCAGCTGCCATCATCTTTTCTCTAGCTTGCAGACACGCACTTATCAAGACTTCCTGTTGGATGAAAGTTTGGTGCTGCCCATGCAATTTGGATAATTGGCTTTCCTTTAACTGTTTGTAACTAAGCTATGGGATTATTGCTGGTGAAGGGAATTGGAGTGCGAACTGATTAATGAAGTCTGTTATCCACGCTATAAGCACTGAGCATGTAGCAGAAGTGCAGGGACTGAAAATGCTTTATGAAACCAACCCAATTTTGCCTCTTCTATGCATTTGTTTAAGAATCGCATTATAGTCATACTTCTTGCATCAGTTGCATTCACAGTATCAAGGCACATGGCCCTTTACACACACACACACACACACACACACACACAGTTCACACCTCTGGGTACTGATGGTACTTGAACATAATAAGCCTTTAAAGGGCCTCTTCCCTCAGATAAAGTGAATAAAACACATTAAAAATGGCTGTTCCAACAGGGAAGACTATCCTGGAGATACTTACACGTCCGTAGCTGCTAAATCTCCAGAGGGCCTTAACAGGAGAGATTTGTGTTGTCTTTGAGCACCTTCTGCTCTGTCCTTTGCTCTTGATGAGCTTCTGCTGCCTGGAGTGACAGCGAGAGGATAATCCAATTTGAATGTACATCAGGAGTTAACTCCAGTACATGACAGTGGTAGAGACAGGGTGACTAAGGTCAGCACAGGCATGCTCTAGCAAACCTGTGAGCCAGACCCAGTGAAACACTCCACCTCTCCACACAGCAGCTTAAATGCTGCTGAGAGGCCATGGGAATCTATCAATGCATCTCCTTGCTCTTAGGAGGCTCTTTGGAAGTTGGCTTGCTTACGCTTGCAACCTGCCAATAAGAAACTGGGCAGAAACCATCATTTGGGCAGCTTGACACTTTTCTTTGGTAGTGGCTGTCATTTGGTACTCATCTTGATGCTATTTGAACACCAAATTCTCCAGATTTCCCTTCTTGTTTTAAGGGTGGAAGAACATTATTTTTTTTTTCAGGTAGTACTGATCACTGTACTCGCATTGTCTTCTTCTTTTTCATTGTCTTCATCAACAG
Seq C2 exon
TTTGATTACTACAACTCCCTCCTGATTAATGAGAAGGATGAAAATGACAATTATGTGGAGCTTGGCGATGAATTCATTCTGGAGCCAAATGAGCATTTCAATAACCTGCTGGTAAACACAACATACAGTGATATCCAGCTCCCTACCAACGTCTACAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013007:ENSGALT00000037501:4
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=0.000
Domain overlap (PFAM):
C1:
PF083996=VWA_N=PU(12.0=70.0)
A:
NA
C2:
PF083996=VWA_N=FE(46.2=100)
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:
GGTTGGTGGAAGCAGCAGAG
R:
CTTTGTTGTAGACGTTGGTAGGGA
Band lengths:
222-1789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]