GgaINT0123789 @ galGal3
Intron Retention
Gene
ENSGALG00000005036 | SH2D3C
Description
NA
Coordinates
chr17:5550042-5550608:+
Coord C1 exon
chr17:5550042-5550344
Coord A exon
chr17:5550345-5550445
Coord C2 exon
chr17:5550446-5550608
Length
101 bp
Sequences
Splice sites
5' ss Seq
GGTGTGGGG
5' ss Score
-6.78
3' ss Seq
CATGAGTGCCAGTGGCAGAGGCT
3' ss Score
-13.48
Exon sequences
Seq C1 exon
AGCCATCCCCTCTGTGGAGCAGACAGCCCAGTCCTGCCAGGATGTGATTGTTTGTCGGCGGTTGGGCTTTTTGTTTTGTGCTGGGCTCTGTTCCTGAGAGGAATCTGCCCTCCGGTACAATACAAATCAGTCCCAAGGCCGTGGCAGCAGCGTCTCCGGGCCACGCTGCTCCCTTTGGAAGATGAAAGGAGATTAAAATGCAATTTTAAATGGAGCCCAGCTGGGAAGCCTTGCTTCCTGCCTTCACAGAGGCAGTGGAACGGCTGCTCCCTCCCTGCGTCTCATCTTCAAGGCCTCTGCGGT
Seq A exon
GTGGGGAGGCCGCTGTCCTGGGGCATGGCAGGAGAAAAAGCACTGAGGCTGGCCTGGTGCCGGGGCCGTGCGGTCTCTGGCCATGAGTGCCAGTGGCAGAG
Seq C2 exon
GCTGTGGCCGTGGTGCTGGGGCTCAGAAGCAGCACTTCCCTCTGCTTGCAGATCGCACGGCTGGAGCAGACCTGGATGGTGCTGAGGCAGCGGCACACAGAGGGTGCCATCCTCTACGAGAAGAAGCTGAAGCCGTTCCTGAAGAGCCTGAACGAAGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005036:ENSGALT00000008075:8
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=0.036
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCCCTCCGGTACAATACA
R:
CTGCAAGCAGAGGGAAGTGC
Band lengths:
251-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]