RnoINT0134570 @ rn6
Intron Retention
Gene
ENSRNOG00000054560 | Sh2d3c
Description
SH2 domain containing 3C [Source:RGD Symbol;Acc:1307287]
Coordinates
chr3:11789456-11790217:+
Coord C1 exon
chr3:11789456-11789571
Coord A exon
chr3:11789572-11790045
Coord C2 exon
chr3:11790046-11790217
Length
474 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TGATCCGACCTCTCTCACAGGTT
3' ss Score
9.37
Exon sequences
Seq C1 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACCCTCCCCCATGGCCGGCAGCTAAGACAAGACCTGCTGGAAAG
Seq A exon
GTAAGGTGCTCTGCGCTAGCCCACGGCTACCTCACGGGCTGTCCCAGGGTTTCTGACCACTCTTCCCACCCCACTAGCCAATCGCAGCCCTGTGGTCCTCGGCTCAAAGCCAGTCTGATTTCCCAAAGACTGCTGTTTATCGACCGGTTTCTCCTCTCGCATCCCCACGTCCGTCAACCTTGGCCTCGCCCACCAACCTTGGCCTCCGCCACCATTACTGTCCACAGTGTTCATTCTAAAACTCTGCCCTTCGGATTTCGCTGATCAATTACAAGCTTCTCCCCCTGGCATCCTGATCTTGCTCCTAACTTATATCGTTCAACCCGGCTCCCTTCGCCTTGCCTGTTACTTTGGCTGCGCCCTTTAGTCCCTGTGACCTACTCTGTTTTCCTTCTCCGCCTCGTCAGCCTTAACAGCAGCTGTGCAGGGGCCCCACCGTATGTCACGCCCCCTCTGATCCGACCTCTCTCACAG
Seq C2 exon
GTTCCACACCATGTCCATCATGCTGGCGGTGGATATCCTGGGCTGCACAGGCTCTGCGGAGGAGCGGGCGGCGCTGCTGCACAAGACCATCCAGCTGGCAGCTGAGCTGCGGGGGACGATGGGCAACATGTTCAGCTTCGCTGCTGTCATGGGCGCCCTGGAGATGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054560:ENSRNOT00000078366:8
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=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(22.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(33.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGGCGTTACCAAGGAGAT
R:
ATCTCCAGGGCGCCCATG
Band lengths:
270-744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]