RnoINT0132819 @ rn6
Intron Retention
Gene
ENSRNOG00000016512 | Sema3b
Description
semaphorin 3B [Source:RGD Symbol;Acc:1310079]
Coordinates
chr8:116354073-116355187:-
Coord C1 exon
chr8:116355048-116355187
Coord A exon
chr8:116354616-116355047
Coord C2 exon
chr8:116354073-116354615
Length
432 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
GTTCCTGCATTCACACATAGGTG
3' ss Score
6.7
Exon sequences
Seq C1 exon
ACCCCTCTCACTCTGTGCTGCTGGAGAGGAAGGTCTTAGGTGTGGAGAGGGGCAGCGCGTTTCTGGAGTGTGAGCCCCGCTCGCTCCAGGCGCATGTGGAATGGACCTTCCATCGTGCAGGGGAGGCAGCTCACACCCAG
Seq A exon
GTGTGCCTCACTCCACCCTTCCTAACCAGGCCCATTTAAGAGAAGCCATCCCCTGCCTAAGGAGGCCTTTGACCTGTACCTCTTACCTATGTGAAATCCCATTCGGTGAGGCCCTGTTCAGATACCCTTATCATAGGTCTCATCCTATTCTGTCCTTAGTTGCACTCTACAACCTAGTGACGCCTCACTGTGCCCAACTAGACTCCTGACCCACCCTCTACTATCTGGAGAGAGAAGGCCCCACGCATTGACGTTTCTAATCTACCCCATGCCCCACTCAAGTGATCCCTCTCACCTAGATCGACTCATCCTCTAAAGGCTACCTATTCCTGTGCTCATACCCTTTAAAATGAGTAAGTGCCAGCACCTATTTTCTTTGTCCACCTTTGGCTTCCAATGACCCTTTGTTTCTGTTCCTGCATTCACACATAG
Seq C2 exon
GTGCTGGCTGAGGAGCGGGTAGAGCGCACTGCACGGGGGCTGCTGTTGCGGGGGCTGCGGCGCCAGGACTCTGGCGTGTATCTGTGCGTCGCGGTTGAACAAGGCTTTTCACAACCACTGCGTCGCCTGGTGCTGCACGTGCTGAGTGCGGCACAGGCTGAACGACTGGCGAGGGCAGAGGAGGCAGCAGTTCCCGCACCACCAGGTCCTAAACTCTGGTACCGGGACTTCCTGCAGCTGGTGGAGCCAGGCGGTGGTGGAGGTGCAAACTCCCTGCGAATGTGCCGCCCGCAGCCCGGGCCCCACTCTGTGGCAGCAGATTCACGTCGTAAGGGTCGCAACAGGCGGATGCATGTCTCTGAGCTGCGTGCTGAACGTGGACCACGTAGCGCAGCTCACTGGTGACTCGGCTGTCCCCATACTGGGGACCAGGCTGGATATGACACACCGAAGAGGGGGCAGATAGATGCCAGGAAGACAGATGAGTTGTGGCTGGGGCACACTGAGATCGTTGGGCCAACGGAGACAACTAACCCATACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016512:ENSRNOT00000066296:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.410
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(9.8=12.8),PF0768612=V-set=PU(47.8=93.6)
A:
NA
C2:
PF0768612=V-set=PD(50.0=34.1)
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:
GGTCTTAGGTGTGGAGAGGGG
R:
CAGGAAGTCCCGGTACCAGAG
Band lengths:
343-775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]