RnoINT0132924 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187810084-187811703:-
Coord C1 exon
chr2:187811531-187811703
Coord A exon
chr2:187810235-187811530
Coord C2 exon
chr2:187810084-187810234
Length
1296 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
CCTTCTCTGGCTGTCTTCAGGCA
3' ss Score
9.83
Exon sequences
Seq C1 exon
AACGACGTAGGCGGTGAAAAGCTGCTGCAGAAGAAGTGGACCACCTTCCTGAAAGCCCAGCTGCTCTGCGCTCAGCCAGGGCAGCTGCCATTCAACATCATCCGCCACGCGGTCCTGCTGCCCGCCGATTCTCCCTCTGTTCCCCGCATCTACGCAGTCTTTACCTCCCAGTG
Seq A exon
GTGAGCAGCAAGGCAGGGAAAAGGAGGGCTGCATTCCAGGGAGGCGGGAGCGGATAGAGCCTACTTTACATTCTGGGCTTTACCTGCGAAGACATTTGAGCATCACCAGACCGGGGGAATCCTACTGTCTCACTCAGAGACTAGCTTCATTCTGGCTGGAAGGCGGACACTAAAAATCAGCAAAAATACCGAGCATCGTGGTGCATGCCTGTGTTCTCGGCTCTAGGAAAGTGGAGGCCAGAGGCTAAAGAATTGGAGCCCAGTTTGGGCTCGACACAGAGATCTTGTCTCAAAGCAAAACATCGATAAAATAAAGCAAGATGTGGTGACGAGGAAGGAAGATCAGGAGTTCAAGGGCTAATGTCTTAAAAATTAAACAAGGGCTGGGGATGTAGCTCAGTGGGTAGAGCACTTGCCTAGCATGTACAGAGCCCTGGGTTTGCTCTCTAGCACCACCTAAGTCAGGGATGGTGGTGCATGGGAAGAAAAGACAGAGGAGGAGCGGGTCATTCTCAGCTCCATAGTGAGGATAACATCGGCTACCAGAGAATGTCTTAAGACAAACAGGACCCATCAATTAGATTAGGAAATAGAAGTAAAAGAAAATTACCAGAAAGGTAGGGAGAGGGTCTGTCAAGCTCAAATGCTATCGAAAAACTAGTCACAAACTTAGTACCCAGCTTCCTAATGGCCATAGTCTATCCCTGAGATTAAGAAAACAGGAAGAAGGCCTTGCTCAGAGACCAAGAAAGGTCCAAAGGTCCCACAGCCACCGTCTGGCACCACGGTGTTCAGACATCTGTTACAATGTATCAGGAAGCAAAGGTTTCTGCTGTGCAGGGTCTGTCATCAGTGAGGAGAGCCCAGTCAGTGTATGGAGGAGACTGAGAAGACATATTGGTTCAACACAGACCAGCAGAAGAGACAAAGTTGTGGCTCATTGTCTGAGGACCACGAAGGAAGCCGGTTCTACCACTCTTCCTGTGGGCACAGCCCAGCCTGGGCAGGATAGGCAAGGGCCACCCCAGGGCCTATGCCCCAATTAATCCTCATTAGAAACAATCAGATTTCAGATTTCAGATCCTGCGATGGGCTTCCAGCCAGGCCTTAGGCAACTCTATGGGACTTTCGGGTCCTTATCACCATAAACAAGGGAAAAAGAAGCCTCCAGAGGTTGGCCTGCCTCCCTGCTGCCCTCCAGGCCTGCTGAGATTCCACTGAGCTCCACTGGGGCTGGAGAGGCAGTGACTGTAAAGCCAAGGAACCACAGTGAATGCCTTCTCTGGCTGTCTTCAG
Seq C2 exon
GCAGGTTGGTGGGACCAGGAGCTCAGCAGTCTGTGCCTTCTCTCTCACGGACATTGAGCGAGTCTTTAAAGGAAAGTACAAGGAGCTGAACAAAGAAACCTCCCGCTGGACCACTTACAGGGGCTCAGAGGTCAACCCGAGGCCAGGCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:9
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=0.235
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.7=100)
A:
NA
C2:
PF0140314=Sema=FE(12.0=100)
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:
AACGACGTAGGCGGTGAAAAG
R:
CTGGCCTCGGGTTGACCTC
Band lengths:
319-1615
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]