GgaINT0005859 @ galGal3
Intron Retention
Gene
ENSGALG00000007388 | SRRM4
Description
NA
Coordinates
chr15:9998880-9999430:-
Coord C1 exon
chr15:9999218-9999430
Coord A exon
chr15:9998997-9999217
Coord C2 exon
chr15:9998880-9998996
Length
221 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
CTCCTCTGTTTCTTCCCTAGCCC
3' ss Score
10.53
Exon sequences
Seq C1 exon
AGGATGCCTGTCCTCGTGTCTCAGCTGTTCAGAGGATAAGAAGCGCAGTGTCCCCCCATCTCCAGCCCGCAGCTCACCGCTCAGGCCGTGCCCCCGCAGCGAGTCGTGCAGCAGCACAGGACGGTCCTCCCCCGGCTCCAGCCGCTCCTGCTCCTCACCCCGCAGGGCCTCCCCCAGGTACTCCCGCAGCAGGTCCTGCTCTTCAGGGAAGAG
Seq A exon
GTAAGGCCAGCACAAATGGCTTTCTCCATCACTCTGGGCAACCTGCGGCTCTTGCAGGCTGGCAGACTCCTTGGGGAGGGGAGGGAGAGTTTGTGTGGGTGCCCAGGGAGCCACGTAGCCCTTGAAATATGGGGCATTTCTCCCCACCACGAGCCTAGATTAGGGGAAGTCTGGTACAACCTCACCCTCCAGCATCTTTAGCTCCTCTGTTTCTTCCCTAG
Seq C2 exon
CCCCAGGTCCTCTTCACGGTCCCCCAGCTATTCCTCCAAATCCTGCAAAAAAAGCCCTGGAAGCAGGAGCTCAAAGACTCGCCGGAGCCCCAGTTACTCCCACTACAGCCCTACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007388:ENSGALT00000011947:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.806 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF152301=SRRM_C=PU(12.1=20.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTCTCAGCTGTTCAGAGG
R:
GTAGTGGGAGTAACTGGGGCT
Band lengths:
305-526
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]