RnoINT0132803 @ rn6
Intron Retention
Gene
ENSRNOG00000023337 | Sema3a
Description
semaphorin 3A [Source:RGD Symbol;Acc:3657]
Coordinates
chr4:18326233-18331379:-
Coord C1 exon
chr4:18331222-18331379
Coord A exon
chr4:18326296-18331221
Coord C2 exon
chr4:18326233-18326295
Length
4926 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTC
5' ss Score
7.46
3' ss Seq
TGATTCTTCTGTGCCCTTAGATT
3' ss Score
9.96
Exon sequences
Seq C1 exon
AAATGTTGGAATCCAACAATGTGATCACTTTCAATGGCTTGGCCAACAGCTCCAGTTATCACACTTTTCTTCTGGATGAGGAACGGAGTAGACTGTATGTTGGAGCAAAGGATCATATATTTTCATTCAACTTGGTGAATATTAAAGATTTTCAAAAG
Seq A exon
GTACTCTTATTACTCTATTCTTTTTTTTAGATTTTTTTTAGATTTATTTATTTTTTTTATTAACTGAGTATTTCTTATTTACATTTCGAGTGTTATTTCCTTTCCCGGTTTCCGGGCCAACATCCCCCTAACCCTTCCCCTTCCTTACGGGTGTTCCCTCCCCATCCTCCCCTCATTGCCACCCTCCCCCCAACAATCAACTGTGAAGATCTTACGTCAAGATTTTTGACAATAGACCCAGAGCTCAGGGCACTGGGCATATTCTAGTAGACTTCAGGGTTGAATAGACTATCAAAAATCTAAAAATTCAGAACCTATCTACTACTTCCCATCAGTGTCTTAGTCACTGTCTTAGCAAGTACTCTTCACCCCTGAGCCAATTGTCCAGACTTAATGGACAAAATAAGTGTTTTAAGGAACTTAGGTTACTTTAACAGAAAATTTCACTAAAATTGGAGAAACAGTAATGGGCATAATGAGAGATTTCAGAGACTAAAAATAGTTTTAAAAACAAAGAGAAATTCTGTGGCTAATAAGTGAATTAAAGTAGATGAAAAAGAGAATAGCAGCAGGAAGTAAGAATATAAATGTGAAATTATTTTAAAACACAGTAAAAGAAGAAGGAGGAATAAATAAATATAAAGAAAAAAATTTTTTGAGGTCCACATCATAAAAAAAAAACACAGAAAAACGAATTTAATTTTACTGTTTTACATCCTGTTCATTACCTACCTCCTGATCACTGACTCCTACAAGTTTTCCCCCATCTCCTTCTCCCCTTCCCCTCTGACCTGGTGTGAGCTCCCCTGGGTATCCCATCACCTTGGCACTTCAAGCCTGTGTGAAGCTAGGTGTTTCCTCTCCACTGAGGCCAGACAAGGTAGCCCAGCTAGAAGAACATATCCCACAGACAGGGAACAACTTTTGGGATAGCCCCATCTCAGTTGTCCAGACCCACATGAAGGCAGGGAGACCTAGGTCCAGCCCGGGTGTGTTCTTTGGTTGGTGGTTCAGTCTCTGAAAGCCTCAAGGGTCCATGTTGGTTGACTCTGTTGCTCTTCTTGTGGAATTCCTACCCTCTTCGGGGCCTGCAATCCTTCCTCCTATTCTTACACAAGATCCCCTAAGCTCCATCCACCATTTGGCTGTTATTACTCTATTCTTAAGCACTGAAGATTTTATGATACTCTACAGCAATTTAATATCAGAACAACATAAATCATTTCAAAATTATTTTTCCAGACATATATAAAATGAATAACAATAATATGTCAGTATATATATTAAGCCATATTATCACCAAGGTTTAAAAATTCATATTACTGTTGATGGTCATTGGAACCCTAAAACAAAACAACAACAACAACAAAAAAAAACTTCTAGCTTTTTCTTCCATGAGTATTTATAGAATAAGATTTTATGGAGAAAACATATACTCTGAAATGTTGGAGAAATATATCATAACTGAATTTACATTACATTGTCCATTGTTCCATATTGTCACCTAGTTAAAGGTTCATCCAGCAATCATCTGATGATCTTCTTGCGTTTGAACATAGTTTTATTTGAATACAGATACTCTCATTTATTTATATGTTTCTATGTTAAATGTTATGACAGAGATGAGTAATTGTAACAAATCACATGGCCCATAATGCCTACAATGTTTGCAATCATTCATTTTAAATAATAAATTTGGAAATCCTCATATAAAATCAAATTTCAGGGCATCAATATTCTTGCAAAATGTATTATTTAGATATCAGAAGGTTGATATTCTTATAAATATTCATTTAGATTTCTGCATCATTTGAACCACTCGATGAAATGTAAAACATAGATTTTTAAAGTAGGCAGAATTGTTTTGCTTCGTCTACGTGCTATAACTGTAAGTCAACCAAATTTTCTTAGTTTTCCAGCCTTAATTCCCTGAGGAAGGAAGTCTTTCTAGAGCAGCTTCGATGAGAACCCCTTAGTGTGTTTCAACTAGCATGTTTCTTCGTATCTCTGGATTTGTCTTTGCTCCTTACCAATGAAGGCATTAATGTGGTTTGCAGAACTATTTATGGAGAACACATTGGATGACAACTTCTTAAAAGTGGATGAACTGTAAAAAGATTTTGTTCTATTTTGAGACATGTTTTATCATTATTATTACATAAACATAAAAATTTATTTACATATATTAAAGTTTTAATTACTATAATATTCATAAAACATTGAAGTTCAAAGATGATATATTTTATAGTAAAAATGAGATATTAAATCATAACCAAAATATTTTTAATCTGATGTTTTTTGAAAACGGGTGATTTCTAAATGTACTCAGGAAATGACCATGTAATGATAAATTTGTCTTTCAATGATTTTTAAATGGTCAAAAAATAAGAAGAAAATTTGTGTGGATATTTCATACGAAGAAATCATTCTTTGTTAAGTAAAGAGAAAATTAGAACATTTGCTATTTTAAATCAAGGATATCTTATTTGTTAAAATTATAAAGATAAGTTTTGTTATTTTGTAAACTTCCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGGTAGGTAGGTAGGTAGGTAGATAGAGAGATGATATGCCCACATACTAGCTCTAACCATGTGAAGTATTTAATACTTTCCTTTAGACACATGTTATGAACTTTGCCATGAAATAAATTGTGTCTGAATGTTAAAAGAACAAAATTAGTCTATCAAAATGCTAGAGATTTGTAAGTAAGAAAGACCCAAGTGTATTATAAGCAAGCATGACAAACTGTGTTCTATTTACAGCACCCACTGAAAGTGCCAAGATCATAGAATAGTCCTGTAATCATCGCTCTTGGGAGATTGAGGCAAGAGGAACAAAAAAAGTGCTGATCAGACAGTCAAGGCAAATCTGTGAGCTCATGGTTCACTAATGCTACAGTAAAAATGAAACAGATAACAATTAAGAATGATGCCCAAAATTAGCTTCGAGAGTCCACACTTCTTCATACACATCTTCACATAAACATATACATATGTAAAGCAGATTATGAAATACCTTAATAATGGAGTCAGAAACTAAGACATTTCTAGTTAACTAGTTTTCAAGTAAAAAATAAAATGTAATATGATTATAAAATTATTAATATTTGAAAGAAGTGAAAAATACAAAATAGACCAATAATTGCTTAGCAAGAACAATTAAGAACTAGTAAAATGAAAAACTTGTGTTTTCTAAAATCAATTTGTTCTAAAATCAATATATAATAAAATTCTTTAATTTTAACACAACTCACCAGAAGTTTGCAATGACATCGAATAAATCTTCATTTACTGTTGGATATAAAAACATTATATTTTATCTGCAACCACTGTGAACTTCAAATTTAAAAGACAAACCCCCCTGACCTCAATTGCCAACGTGAAGACAGATGGCCATGGGATTGTCCTGTAAAATGTCAAGGTTCAGGGTGATGTTCATTCATAAATATGATCAATGAGGTATTTTTGAATGTCTTCAATATGTGACTACATTATGTGGAACAGGTTTTATCTCAGTTTTAATTTAGACACACAAACACATATGTGCAGAAAAATCACCTAGAAGAGAACGAACAAATTAAGAACTTAGTAACAAAAAATGATGAATTATCCATTGTATTCTTAAATATCATATTTGTGATATGAACTGGAAATGCACTTCTCAAGGAATCATATGTTATTTCAATGACTCCTAAACTCTTGTTTATAAGTATGCTGCACTTGGGGTTCCAATTCCCTAGGTTGAAATCTCAATCTTTACCTGAGCTTGTGACCATTCACGGTGAATTATCTTGAGGCTTCAAATGAATGGTAATCAATCATTCAGAGACTAAAAGCTTTCTGGCACACATAAATAATAAACTGCCACTGACTCTGGATTTTTATTTAATGTATGACATTTCCCCCTGGAAATTAACAAATATAACTAGAAGAGAAAACTGATGGAGAAATAATAACTTGTTCTGCCCAGTGGAGAAGAGACCTATTAAAATTAAAACCCATGGAAAATTTTTGGGACTTGGAACTTGGAAAATTTTGGAAGAGAGTATATATATTGCTATTATAGAGAAAATGTATTCAACTGTCTAAGCCACCATCAGTAGCATCATGACTCGTCTACTGTGACTGGATCTATAAGAAATGAAGTCCTGGGAAGTCTTTCAGCTTCCCATGTACTAGGATTATAGCTAATAAACACTGTGCCCAGTCAAAGAAGAAGTCTCTCAGAACTATAATTTTTCTTTGTTTTCACTTTTATCATCTCAAAACATATGTTGTTATTTTTCAATATTTCTTATTTTCACATTGAGAGAGGAAGAGAGCAAACAAGAAAGAGATTACTTTATGAGCTGTATTTTTCAAATATTTCAGGTCTCACCCTTTATTGCCATGCTAGAATTTGGTTCAGAGAGCTATATTCAGAGTACCCTTTTGTTAAATTCTCAAAATCACTATTTCACAATGACTACTGGGAAATTTAAAAGAATGGGAGTCATGTTCTCTGCCAGTTCTCACGTAGATCTTCATATTTTCCAGGAAGATCTTTGTTTCCCATGCAGTGTAGCAGCTCTGTTCATACTGTACTGCTCAGACCAATGAATCCCTTTAATAGGTTTCCAACTCTAGTTTGATACAGTGCAAAAAGTAGTTTATAGATGGCGAATGCAAGACCTTAGTATATAGAAATATATTAGCTATTATTAAAAGAAAGTCAAATTTAAGAGATTACTGGATATAGTATTTCTCTCCCTAAGCTGTACCTAACAAATATAAAATTTTATATATATATATGTATATATATATATATATATATATATATATATATATATATATATATGATCTCTTGACAAATTTAATTGCATGAAAATGTGATTCTTCTGTGCCCTTAG
Seq C2 exon
ATTGTGTGGCCAGTATCTTATACCAGGAGAGATGAATGCAAGTGGGCTGGAAAAGATATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023337:ENSRNOT00000034692:2
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(7.5=62.3)
A:
NA
C2:
PF0140314=Sema=FE(4.5=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]