GgaINT1025024 @ galGal4
Intron Retention
Gene
ENSGALG00000005036 | SH2D3C
Description
SH2 domain containing 3C [Source:HGNC Symbol;Acc:HGNC:16884]
Coordinates
chr17:4920746-4921193:+
Coord C1 exon
chr17:4920746-4920861
Coord A exon
chr17:4920862-4921021
Coord C2 exon
chr17:4921022-4921193
Length
160 bp
Sequences
Splice sites
5' ss Seq
ACGGTACGG
5' ss Score
9.91
3' ss Seq
TGCCTCTCGCCCTGCAACAGGTT
3' ss Score
6.83
Exon sequences
Seq C1 exon
GTTGCTCGGATATTGGGCGTAAGTGCAGAGATGCAGCGGCTCATGGGGGTGAGCTCCGGCATGGAGCTGCTCACCCTGCCCCATGGCCACCAGCTCCGGCTCGACCTGCTGGAACG
Seq A exon
GTACGGCACAACCCAGCTCCTCTGGGGTGCCCCAGCTCGGCACAGGGGGACATCACATCTCCTGGGGTCCCGCTGAACCCCCATGCTGGGGCAGTGGCAGGAGCACCCCCAGCTCTTTGCCCCCACGCTGAGCCCCGCTCTGCCTCTCGCCCTGCAACAG
Seq C2 exon
GTTCCACACCATGTCCATCATGATCGCCGTGGACATTCTGGGCTGCACGGGCAGCACAGAGGAGCGGGCGGCCCTGCTCCACAAAACCATCCAGCTGGCTGCCGAGCTGAAGAGCACCATGGGCAACATGTTCAGTTTTGCAGCTGTGATGAACGCCCTGGAAATGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005036:ENSGALT00000008075:9
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:
PF0061714=RasGEF=FE(25.0=100)
A:
NA
C2:
PF0061714=RasGEF=FE(37.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGCTCGGATATTGGGCGTA
R:
ATGTTGCCCATGGTGCTCTTC
Band lengths:
245-405
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]