RnoINT0134569 @ rn6
Intron Retention
Gene
ENSRNOG00000054560 | Sh2d3c
Description
SH2 domain containing 3C [Source:RGD Symbol;Acc:1307287]
Coordinates
chr3:11787960-11789571:+
Coord C1 exon
chr3:11787960-11788082
Coord A exon
chr3:11788083-11789455
Coord C2 exon
chr3:11789456-11789571
Length
1373 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGT
5' ss Score
9.57
3' ss Seq
CCCTTTGGGCGTCTTTGCAGGTT
3' ss Score
9.67
Exon sequences
Seq C1 exon
TCCCAGCTGATCCCCAAGGAGAACCGGCCTCTGGAGGTGGGCCTGCTGCGCAAAGTCAAGGAGCTGCTGTCGGAGGTGGATGCCCGGACGCTGGCCCGGCATGTCACCAAGGTTGACTGCCTG
Seq A exon
GTACGTGTTAGGAATGCTTAGGGAGGGGACAATACCTTTAACATCTGGCTTTGAGGTCAGGAGTCAAGATGGTGACGGGCTGATTTCAAAATTCCCCAAGTACAATGACGCCAGCAGCCTGAGTTTTGACATCCCAGGTGTCTCAGGCCCCTTTTTCAGATTTATTTATTTTATGTATGTGAGTGCACTGTCGCTGTCTTCAGACAGACACACCAGAAGAGGGTATCAGATCCCATTACAGATGGTTCTGAGCCACCATGTGTTTGCTGGGAATTGAACCCAGGACCTCTGGAAGAGCAGTCAGTGTTCTTAACCACTGAGCCATCCTTCCAGCCCTCCATTTTCTTATTTTAGATTGTTTTGTTAGGGTCTCACTATGTAGCCTTGGCTGGGCTGGAACTAGCTGTGTAGATGAGGCTGGCTGCTATGTAGACCAGGCTGGCCTTGAACTCATAGAGAGCTTCCTGTCTCTGCCTCCCAAGTGCTGGGATTGAAGGCATGAGCCACCACCCCTTGCCAGTCTCCTCCTCCTTCTCATTTCATTTTTGATGTGCACTGGTGTTTCGCCAGCACGTATGCCAGGACTAGAGTTATAGGCAGTTGTGGACCACCATGTAGTTGCTGAGAATCAAACCTCAGTCCTTTTGGAAGAGCAGCCAGTGCTCCTAACCACTGAGCCATCTCTCCAGCCCAATTTTCTTCTTTGGAAAAGTGACATCCAAGGTATTTCTACAGCCTGCAGATGTTGGTTTAGAATGAGAGATGACGTTTTGGGGGTAACTTAAGGAACATCCTGGTTCTAGTCTATATAAAATGAACATCTGGTTGGGGGGGGCATCTTCTCCCTTGACCCCACATTTCCTAGTGGACAACAAGCAAAACATTCCCTGGCCTCAAAACTGTCCCCATGCCAGTGTGAGGCACTGACTCCGCTAAGAATCACAGCTCTTTGCATACCTCGGTTTCTCTGTAGTTTCATATGAACGCTGCCTGCTGAGAAGAGGGAGGAACTGGGTTGCAGGCTCAAGTGTATGAACTTGAGCAAGAGAGTCCGTTCCCTTCCTGGGCTTTGGGTTGGCAATCAGGATAATGACATCCTGGCTCTTAATCTTGAGTAGTTAACATCGCACACACCTATGGGCATCTGATCTTCCTACTCCCCATTTTACAGATGGGGAAACTGAGGCTCACTCAGAAAGGGGGAAATTGCTACGTGTTCACAGAGGAGCTGGGATTCAACCCCCACCCAACCCTACTCCACCCCACCCTCTGAACCCTATAGCCAGGCGACCCTCTTAGATGAAGCTCTGACTCCCAGATGGCTTGGACCAACCCTGACAGGAAATTAATCAGCCCTTTGGGCGTCTTTGCAG
Seq C2 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACCCTCCCCCATGGCCGGCAGCTAAGACAAGACCTGCTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054560:ENSRNOT00000078366:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.683 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061714=RasGEF=FE(22.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCAGCTGATCCCCAAGG
R:
TTTCCAGCAGGTCTTGTCTTAGC
Band lengths:
238-1611
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]