GgaINT0120281 @ galGal3
Intron Retention
Gene
ENSGALG00000013007 | CACNA2D4
Description
NA
Coordinates
chr1:63193026-63195254:-
Coord C1 exon
chr1:63195176-63195254
Coord A exon
chr1:63193160-63195175
Coord C2 exon
chr1:63193026-63193159
Length
2016 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
GCCTCTGTTTCTCCATGAAGGCT
3' ss Score
7.61
Exon sequences
Seq C1 exon
GTCCGGGTTTTCACTTACCTCATTGGACGGGAGGTCACTTTTGCCCCCAACGTGAAATGGATCGCTTGCAACAACAAAG
Seq A exon
GTACTGTACTGTAATGGCTACCCAACTCCAACCAGACACCTTACATGTGGACCGTGACTGCGGGTCCATGGACTCCCCCATTAGTTCCCAACTACAGCTGGGGCCCAGGAACCATTGGTTGGAAGATGACCTAAGGAAAGAGCAGGCCCTGCTAGTCTGCGTGGAGTATGCCCATGTCCAGCTAATGCAAGTCCTCAGTGCTGAGCCACCATGTTTTCCTGTCTTGGTGCCAAGGGACACTGTGACCGAGATTCATGCCAGCTGTAGTCCACCTAAGTCCCTCTGCTTATTGTGTTCCAGCTGCTGGCTTTTGACAAGCTGTCTAAACCTCTGTCAGTAAGCCTGACATCTTTTGACTCAGATGTAAAACAAGCATATTTTTTAAGGATTTTACTGCATTTTATGCAATGCCTGCAGGTTAACCCCTATATGCCAGCCAAATTCTTTGTGTGCCAGTGATTTCACTGAGGTACCAGGACAGCTTGCTAATTCTGCCTCAAAACCAATGTTCTCTGTAGCCAGCACGAAATGGCATGAATGGGAAAGCTCATTCAGAGTAGATAAGTCATCCCTACCCATTTGAGGCCAGTTTAGAAGTCCAGTTAGACCAATCAGACATGAGAAAAGAAAGGGAAAAAAGGTCTTGTCTGTTTGGGCTTGACTTGGCCCTAGTACATCTGGAGATGGCCAGCAACCTGCAGTGCTTGCTATGTCTGTACACTTTTTCAACAGAGAAAGGAAAAAGAGACTGAGGTTGGGCCCTGACCACTTGGGGTTATTGGATCTCTTTCTGTCTGAACAGTGTCCTCAACAGACTGTGTGAAAGATAGCGGTATATTTGCTATTGAAAATAATTGACATACAAGAGTTGCTGATCTGTGGAGTGTACACATGCTGAGGATGTCCGAGGTTCAAATGTTTAACTGTTAGCACTATGAAACACAATTAACATTTTTTACTTTTTACTAGATGAAAAAAAAAAAAAGGATTTCAGATTGCAGATTCAACTGTAAGATTAGTGACAAGAAATTCACAGTACTGTTGGTTCACTATAAAATGTGAGAATGGATTATCCTTGAGAACAAATATATACTCTTCACACTTCAATTCTCACTTAGCAAACTCGATCTCCAAGGAAGGCTCACTGATCTTGGCTCTTCCATTTCAACATATTATACAGCTCTTTAATCCTCATTTTCAAGCACACAAAATGTTTCCACATCACAAAGCTTATCAACTCATGAGCCACTTCACATGGCATTGATTTCCTAGTGATAACAATTTTCCATATACTTGACATACTCTGTGCTACACCAAGTGTAAGCAGTGAGATCCATGTTTAGCATTTCTAACCAGCTAAGCAGCTAGCATTTGACAATCTTTTGATAACTGGAAGACATTCTTTCCTTGTACTCTTTGCTGTATATTAGACTGCTATGGGTCCATCTGTGGAGAGAAAGCTCTGGAAATAGGTAACTTACACTTTTTGGTTCTGCTTCCAATGGGTGGATAGACATAGTCCCCATCCTTGGATGCAAAGCGAGGCAAAGCAAAGAGTAGAGCACTGTGGAAGAGAAGCTGAGAGTTTGGGTTTCACATAAAATGGGACAGGGAAAGTGAGTAGCTTGGTGGAATACCTTCTTTTGTATGTTTGGCATTCAGGACCACAGGCAGCCTGATTCATTCGTGAATGTTTTTGCCTAAGACCTAAAATAGCCTTTTACATCTGCTTGTTGTGGCTGCTGTTACATCAAGACTCTGGTCTTGAGTACTGGTCCAGTGGTTTGAGAAGAACAGAGCGAGCCAGTGCTTTGAAACTCTAGATTTCCATGGAAACTTGTTTACATAGCAAAGCATGGCTGCAAGGCACGTCAAGGCGCTTTTTGTAAAGAGCGGATAAAACTGTCTGGGTAGATGCAGTTTTTACATACTGTTTTCTGACTTCACACGAACACTCATTTGTAAACGTGAGGGATGTGTCAGAAGAGTGACTCATGCCTCTGTTTCTCCATGAAG
Seq C2 exon
GCTACTATACCCAGATCTCCACACTGGCGGACGTCCAGGAGAACGTGATGGAGTACCTGCATGTTCTCAGCCGTCCTATGGTCATCAACCATGACCACGACATTATATGGACTGAAGCCTACATGGACAGTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013007:ENSGALT00000037501:11
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=0.000
Domain overlap (PFAM):
C1:
PF137681=VWA_3=FE(15.7=100)
A:
NA
C2:
PF137681=VWA_3=PD(2.4=8.9),PF0274313=Cache_1=PU(8.0=17.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]