GgaINT0120293 @ galGal3
Intron Retention
Gene
ENSGALG00000013007 | CACNA2D4
Description
NA
Coordinates
chr1:63170203-63172039:-
Coord C1 exon
chr1:63171944-63172039
Coord A exon
chr1:63170331-63171943
Coord C2 exon
chr1:63170203-63170330
Length
1613 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TCTCCGTTTTCTTCCGGCAGGAA
3' ss Score
11.01
Exon sequences
Seq C1 exon
GGAGTCTGAGGCAGGGGTTGAGATGGCATTTCTGGGCACTCGGGCTGGACTCATGAGGAGTGCCCTGTATGTGGGCTCTGAGAAACTTTCCAACAG
Seq A exon
GTAAGTCCCTAAGCTGCACTAAGGGATTTCTCTGTGTCTCCGAAGGTGTTTCCAAAACTACTACCAGACTTAGAAATGTACTTGAGGGTACAGAAAGGAAAAGAGCAAGACCTTGGTGGCATGGGAGCTGATTTACGGAATCAGGGCATTCAGTCCTTTGTGTTGCTCTGGTCCTTTTGATTTTTTTCCTAAAGTGCTGTCCCAAAGTGCATTAATTTCATTGTAAAATAAGAAACTTCTATTATTCCCCGACTTCAGTCAGCTAAGAGAGAAAATGCCCATCATTATTATATATCCCCAGGAGCATTCTGTAATGTAAAGGCTCTGCACTCCAGTGCCCTATGACATCCCAGCTTGGCTAGGTTTGATCTTTCTGTCTCAGTTCCTCTCTGTTTTATTCTGTTCTGGCTCTCACATGGCCCACATCACATTACTATCCCAGCGTCTTCCAGTGATGCATTAAGTGATGTGACTGACATCTGTCATATATGATTCATTCTCTGTCCTCTCCCTTAAGGCAAAAGTGCATGTTCAGTGGAGGTTTTTGACATGGAAAGGGCATTGATTTTTGTTGTTGATGAGTTTCGAACATGCAGACTGATACGTGAAAGGACAGGTTGCAGAGGCAGATGGAACAACAGGATGGTGGTGGTGGTCCTTAGCTTCTTGGCAGGTGTTTCACTGTCTCCCACTTTCTCAAATATGAATCATATGTCCAAAGCAGAGAGCTGCACTGTGCAGCCACTCTCGCCTTGTTTCTGAGACAGTCTTGGATAACTCGGAGTACTCAGGCTTTGGTGTCAAGGAGGAAAGAGTGCTATAGAAAGCTAATAGAATAACTCTGTAGCCCATGCTGCTCATCAGGAGCGTTGCTCAGTGCTTCCGAACAGTTGTAGTCACTACATTTCAGTGACAGATCCCCGCATGTCACAGGAGAGGCACTTTTGGGATCTCTTGAAAGGAAGGAATTGTATAAATGAGTAACTGTTGTTATGACAAAACATTCAGCAAAAGGAGAGTCTGAAAATAAAGGGGATTTGTCAGCCAGGAAGGAGAGCTCTCCAGGGAAGGCAATGACCTGATTTTTACCAGGGCCCTCCTGAGCTGCCTGGCGGGCCATGCCCTCAGCACCCATCCTCTGGTCTTCAGAAACACCCGTTTCCCCAAGTTCTTCAGTCCGCACATCACTAGGAGTTCAATATCTAGCGCCTCGTTCCCCCCCCCCCCCCCCCGGCCCTGCACGGCTCTCCCGCACGGCGGCCCACGCTGCATCCCAGGGGAGAGGTGGAGGAGGAGGAAGGGGACGTATTCCCAGCGCTCAGGCCCGTTGCCAAGCCCACAAGCCGAGGCAGTTCCCTCGCTGTCCACCCTCAGGGCCGCGACCTCCCCTCGCCCGTCCTCGGAGCTGGTGTAGGGGCGGTGGCGGCGCCGCGGGCCTCGGCCTGGGCAACAGCGGCACCTGGCGGGCGGCTGGCAGCGGCGCGGCGGCCGCGCTGGCCCCAGAGCGGCGGGGAGCGGGGCGGGGGGGCTGCCGGGCCCCTAGGCTTGCAGAAGGCGGCTCCCCGAGCAGAGCTGCCTTGTGCAAAAGGCGACTCTCCGTTTTCTTCCGGCAG
Seq C2 exon
GAAATTCCTGACTCGGAAGGACAAAGAGAGTATCTTCACCATGGACCACTTCCCTCTGTGGTACCGCCGGGCAGCTGAGCATCCCCCCGGGAGCTTCATCTACAGCATCGTTTCAGAAGATGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013007:ENSGALT00000037501:23
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:
NO
A:
NA
C2:
NO
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:
GAGTCTGAGGCAGGGGTTGAG
R:
TGAGTCATCTTCTGAAACGATGCT
Band lengths:
222-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]