RnoINT0132913 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187801971-187803194:-
Coord C1 exon
chr2:187803014-187803194
Coord A exon
chr2:187802090-187803013
Coord C2 exon
chr2:187801971-187802089
Length
924 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ACCTTGTCTCTGTCTCTCAGCTA
3' ss Score
9.39
Exon sequences
Seq C1 exon
TGCTCCATGGGCCCCTCCTCTGACAAAGCCTTGACCTTCATGAAGGACCATTTTCTGATGGATGAGCATGTGGTAGGAGCTCCCCTGCTGGTGAAGTCTGGCGTGGAGTACACACAGCTTGCCGTGGAAACAGCTCAGGGCCTTGACGGGAGCAGCCATGTGGTCCTTTACCTGGGTACCT
Seq A exon
GTGAGTATGGGCTTCCAGAATATACTTGGGATGACCAGAGCAGGGGCCCAAACCCAGGCTGAGGCAGGAAGCCTTCGAGGCCATCCATGTGTTCAGTTCATAATTTAACAGATATTTAGTGTGTGAGCCCCCTGCTGGACATAAGAGGCACAGTCCCACAGCAGGACATCCAGTCTCTCCCTGAGCTTTCAGTCAGCAGGGAATATAGACCCCAATCTATAGTCCAGTCTTAGAAAGCGCTGCCTGCCTTCTGGGAGGAGCCATATCAAAGGCAGGAGAAGTGATTGGGGAGGGATGCTTGACTGAAAGGAGCATCAAGGGTGACCTGAAGAAGGGTAGAGCCGGCCACCCCCAACCTTTTCCCTATCCCCCAGTCTCATGAAGCCTGTGCTGGTCTCCTACTTACTATGTGGCTAACATTGACCTGAACTTCTGATCCACCTGCCTCTAACTCCCAAGTGTTCGAACTGTAGAATAAGACCCTGTCTCAGGGAAAAAAAGGAAAAGAAAAGAAAGAGAAGGAAAGGAAAAAGAAAAAAAAAAAAAGAACATGGAGTGGTGGTACATGCTTTTAGTTCTAGTATGTGGGAAGTAGAGGCAGGCAGATCTCTGTAAGTGTTGGGCCAGCCTAGTCTACTTAGTGAATGTGAGGCCAGCCAAGGGCTACACAGTGAGACCTGACTCAAAAAAACAAAAACAAAAAAAAACAAAAACAAAAAAACAAAAACAAAAAACAAAAACAAAGTTGGCAGCTAGCCTGAGCAGCAGAATGAGACCCTGTCACTAAGGAAGGCAGACCACCACCACCCCTCCATCCCCGGGCTGTGGAGGGACTGAGTGACCTGCATGCCTTGTGCCCAGCTTGCTGGGGAGGTGTGTGAGGTCAGTGACGGGAGGAAGTTCTACCTTGTCTCTGTCTCTCAG
Seq C2 exon
CTACGGGGTCCCTGCACAAAGCTGTGGTGCCTCAGAATAGCAGTGCTTATCTTGTGGAGGAGATTCAGCTGAGCCCTAACTCTGAGCCTGTTCAGAACCTGCAGCTGGCCCCCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.066 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(9.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCATGGGCCCCTCCTC
R:
CAGCTGCAGGTTCTGAACAGG
Band lengths:
286-1210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]