GgaINT0120273 @ galGal3
Intron Retention
Gene
ENSGALG00000013007 | CACNA2D4
Description
NA
Coordinates
chr1:63208468-63210257:-
Coord C1 exon
chr1:63210198-63210257
Coord A exon
chr1:63208631-63210197
Coord C2 exon
chr1:63208468-63208630
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:ENSGALT00000037501:3
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
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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]