GgaINT0098824 @ galGal3
Intron Retention
Gene
ENSGALG00000008654 | STAM
Description
NA
Coordinates
chr2:19582372-19583199:-
Coord C1 exon
chr2:19583104-19583199
Coord A exon
chr2:19582519-19583103
Coord C2 exon
chr2:19582372-19582518
Length
585 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TAATTTTTATTTTTCTATAGGGT
3' ss Score
9.18
Exon sequences
Seq C1 exon
CTTCTAGGAGCATGTGTATCAAACTGTGGCAAAATCTTTCATTTAGAGGTCTGTTCAAGAGACTTTGCCAGTGAAGTAAGCAATGTGTTGAATAAG
Seq A exon
GTAATGTACTGCATTGATTTATATGATTCATATAAAAGTTAAATCAGATTGATAACTGGGGTAACCTGAGATTGGAATGGAATCTACTTCTTGAAGACTGGAAGTTTTGGGAAGTGAATACAAGAAGAGGGGGATTTGAGAGAAGCATAAAAGATTAGTGGGAGGACTGACTGAGAAAGAACTTTCTGACTGCCACTTCATACTATGGTTACTTGTGTATTCTGTTCATGTGTGGAGTGAGATTAATTGGTAAATGCCTACATTCATTTTCACATTTAATAAAAACAATAGAAGACTAAATACAGACATGCAGTGAAGTGGAGATGATAAAAGGCTTTTCTGTAACTTTGTATACAGTGCTTTTTGGCTAGTCCGTATTGTTGAAATGCTATTCCCAAAGGCCATTAAACATGGCGCTGAAAGCTGGTGTACTCTTCTCCCTTTCTAATAAAAGGTATCACTTAGCAATGTACTGTGTTGTCAAGTGTACGTATAGCTGATACTGAAAGTAGCATGAATGTATGTGAAACGAAGGAATTAAGAACAGATTCCTATGTTATTTGATTAATTTTTATTTTTCTATAG
Seq C2 exon
GGTCATCCAAAAGTTTGTGAAAAGCTGAAAGCCCTTATGGTGGAATGGACTGATGAATTCAAAAATGACCCACAGCTTAGTTTAATATCTGCTATGATAAAAAATCTGAAGGAGCAAGGAGTTACTTTCCCAGCTATTGGTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008654:ENSGALT00000014097:4
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=0.020
Domain overlap (PFAM):
C1:
PF0079014=VHS=FE(23.0=100)
A:
NA
C2:
PF0079014=VHS=PD(28.9=79.6)
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:
AGGAGCATGTGTATCAAACTGTGG
R:
CCAATAGCTGGGAAAGTAACTCCT
Band lengths:
231-816
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]