RnoINT0134565 @ rn6
Intron Retention
Gene
ENSRNOG00000054560 | Sh2d3c
Description
SH2 domain containing 3C [Source:RGD Symbol;Acc:1307287]
Coordinates
chr3:11782749-11784411:+
Coord C1 exon
chr3:11782749-11782877
Coord A exon
chr3:11782878-11783956
Coord C2 exon
chr3:11783957-11784411
Length
1079 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTTCTCTGTACCTTCTGTAGGTC
3' ss Score
10.13
Exon sequences
Seq C1 exon
TTCTCCAAGGAGAAGTACATTCTCGACTCCTCGCCAGAGAAGCTGCACAAGGAGCTGGAGGAAGAGCTGAAGCTCAGCAGTACAGACCTCCGCAGCCATGCCTGGTATCATGGACGTATCCCTCGTGAG
Seq A exon
GTGAGCAGGCCCCAGGCAGGGATCTCAGCCCCGGACCCTTCCACCCATACCTTGGCCAATCCCACCCTGGGCTCCAGTCACCAGACAGTCTCTGTCCTGATCGTCGGCAAGGATGAGGCTTAGCTTTACCATCGACTGTGTGACCTTGAGAGAGTCACCTTGCCTCTCCAGACTCCAGCATCCTCATCTGTAGAATGGAGAGATAGCCCCTCAAGAGGCAGTTGTGTTCCAGGTAGTGGGACCCCGTCTCAAAGGGTGGGGCTGTTGCGAAGGTGAAATGAGCAAAGGCAGGCAGAGTGGGTTGTCTGTTGGTGGATGCAAGCAAGGGGTGGGGGAGTGTTGTTACTGTGTTTTATAGCTTAACCTCCTGTGGATTTGGTTAGAGAGTATCCGTTTTCAGGCCACTCGATTTTGACTAAATTTGGGTATCTGGCCTGAGGTGACTTTATGAGTCACAGACCTGGACTGATGGGTCACCTGACCCTTTTCCCCCTACACAGGGGATCCAGGATGTAGAGAAGTTAAGGTGGCAGCTTCTTTGGAGCGAGCATGCTGGCCCCAAAGGGCACAGAGTATCAATCGTTTCACAGAGGTGTAAGAATGGGGTGCTGCACAGAAATGCAGGTAGTCACCAGGAAGGGCACTGGATGGAGCCCTAAGGAGATGTGTTCTAGGCAGAGAGGGCATCTCAAAGGAGCAGACACCCAGAGCTGTGCAGGGGCCTGGATGGGTGCAGGAGAGAAGGCCTGGAACCCACTTTGCCTTGTTGGAACCCTGAGAGGGGCTGGGTCTGAGACCTAAGCCTCTGATCACAGAGCTTTCAGCATTTCCAGTCACTGTGTCTCTGTCTCCATTCCCAAGTGCCACCTTCTGCCATTCCTGGGGCCCTGTGTCCCTGACTCATGGCCTCAGCCGAGGTGTCACCCCAGACTCTGGTCCTAAGCACCAGATGTCTGATGGCTATGAACTGGATCCTCCATGCTCTAGATGGTGTCTCGGTGTCCCAGATTCCAAGTCACCCTATCCCCTGCCCCTCTCTTCTTTAGCGGCCGCACCTAACTTCTCTGTACCTTCTGTAG
Seq C2 exon
GTCTCCGAGACCCTGGTGCAGCGGAACGGCGACTTCCTCATCCGTGACTCTCTCACCAGTCTGGGGGACTATGTGCTCACGTGCCGCTGGCACAATCAGACCTTGCACTTCAAGATCAACAAGGTGGTGGTGGAGGCTGGCGAGAGCTACACCCACATCCGGTACCTCTTCGAGCAGGAGAGCTTCGACCACGTGCCCGCCCTTGTGCGCTATCATGTGGGCAGCCGTAAGGCCGTGTCCGAACAGAGTGGGGCCATCATCTACTGCCCCGTCAACCGCACCTTCCCACTGCGCTACCTCGAGGCCAGCTACGGCCTGAGCCAGGGCAGCAGCAAGGCTGCCAGCCCAGCCAGCCCCTCAGGCCCCAAGGGCAGCCACATGAAAAGACGCAGCGTTACCATGACTGATGGGCTCACCTCTGACAAGGTCACCCGCGGAGATGGCTGCCCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054560:ENSRNOT00000078366:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.081 A=NA C2=0.283
Domain overlap (PFAM):
C1:
PF0001719=SH2=PU(9.9=18.6)
A:
NA
C2:
PF0001719=SH2=PD(87.7=46.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAGAAGCTGCACAAGGAG
R:
AGATGATGGCCCCACTCTGTT
Band lengths:
358-1437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]