GgaINT0123785 @ galGal4
Intron Retention
Gene
ENSGALG00000005036 | SH2D3C
Description
SH2 domain containing 3C [Source:HGNC Symbol;Acc:HGNC:16884]
Coordinates
chr17:4917269-4918016:+
Coord C1 exon
chr17:4917269-4917397
Coord A exon
chr17:4917398-4917567
Coord C2 exon
chr17:4917568-4918016
Length
170 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GTCGCCCCATCCCCTGCCAGGTC
3' ss Score
9.36
Exon sequences
Seq C1 exon
TTCTCCAAGGAGAAATACATCCTGGACTCGTCACCGGAGAAGCTTCACAAGGAGCTGGAAGAGGAGCTGAAGCTGAGCAGCACCGACCTGCGCAGCCACGCGTGGTACCACGGCCGCATCCCGCGGGAG
Seq A exon
GTGAGGATGGGGAGGGCGGGGGCTGCCTGGGTTTGCCACGGGGACACTCCTGGAGCTCCCAGCCGGGATGAGGGAGATGCCCTAAATAACAGCCCTGGCGGAGCATCCACCCCCATCCACCGGTACGGCCAACGGGGCCGTGTCTGAGCTGTCGCCCCATCCCCTGCCAG
Seq C2 exon
GTCTCAGAGAGCCTCGTGCAGAGGAACGGCGACTTCCTCATCCGCGACTCGCTCACCAGTGTGGGTGACTACGTGCTGACGTGCCGCTGGCGCAACGAGCCCCTCCACTTCAAGATCAACAAGGTGACGGTGAAGTCCAGCGACGGCCGTACCCGCGTCCAGTACCTCTTCGAGCAGGAGAGCTTTGACAACGTGCCCGCCCTCGTCCGCTTCTACGTGGGCAACCGCAAGGCCATCTCCGAACAGAGCGGTGCCATCGTCTACTGCCCCATCAACCGCACCTTCCCCCTGCGCTACCTGGAGGCCAGCTATGGGCTCGCCAATGGGAAGCACGGGGGGTCCCACAGCCCGGCCTCCCAGAAGGGGGGGCACATCAAGAGGAGGAGCATCACCATGACAGACGGGCTGACAGCCGACAAGATCACCAGGGCTGAAGGGTGCTCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005036:ENSGALT00000008075:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.256 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0001719=SH2=PU(9.9=18.6)
A:
NA
C2:
PF0001719=SH2=PD(87.7=47.3)
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:
TACATCCTGGACTCGTCACCG
R:
CTGGACTTCACCGTCACCTTG
Band lengths:
254-424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]