GgaINT0110278 @ galGal4
Intron Retention
Gene
ENSGALG00000006560 | SEMA3A
Description
semaphorin-3A [Source:RefSeq peptide;Acc:NP_990308]
Coordinates
chr1:8729292-8732881:+
Coord C1 exon
chr1:8729292-8729449
Coord A exon
chr1:8729450-8732818
Coord C2 exon
chr1:8732819-8732881
Length
3369 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
TTTTTTCTCTGTGTCTTTAGATT
3' ss Score
11.42
Exon sequences
Seq C1 exon
AAATGTTGGAATCCAATAATATAGTCAATTTCAATGGACTAGCTAATAGTTCCAGTTACCATACTTTCCTCTTGGATGAAGAACGAAGTCGGCTGTATGTTGGAGCAAAAGACCACATATTTTCTTTCAACCTGGTTAACATCAAGGAATATCAAAAG
Seq A exon
GTACAGTTAGTCATGTTTTATATGTTTTATATGTTTCACATTTTTGTATAGGACTATATGACTTATGTAGTAAGTGATTGTATATCAGGAATACTACTATGGCTAAACAGCCAAACATTTCTCAACTCTATGGAGAGAAAAATATTATGAGCCTATAAGTGTTGAATAATTTTTACTTTCCCCAACTATGGAAATTTAAGTCATAAATGAATAATCCAGCTAATTTGTGAACAAGACATACTTCGTATTTGCTGTTAAAAACAAACATACAATTATGAAAGTATACAAAAAAGGCCTCATTTTTCTTCATTTGCAGATGGAAAGAATCTATTCACGAGTCTGCGTTGATTTCTTATTTTTAGCCCAGCGCTTTAAAGCAATTTACTCCTGATGCTCATAAACCAAAATAGATTAAGTATTAATAAAAGAGAAATAGATTTGTACAAGCTTTGTATTCTTGAAGAGAAGTATAATTTTCCAGTAAAAGTTGGAGACAAATGAAAATTTGACAAATAGTTCAGTGATGTTCTGGAATATGCTTTCTTGAAGCCTAAATAAAACATTTTCTTTTCTAATTTACTTTATGATACAAAACACTAAGAAGGTAAACTTTAAGTATTTTGATGGCACATTTTAAAATACAGGGAGTACTCTTTTGGGAGAGATATACTGCTTCAATACCAGGGCATTTTTTTCTTGGTGTTCCTGACCTTTTGCCCGTTTCACTATTAGCTTCCTAAGATGATAGCAATAAATACCTTGTGTTTTTTGTTCAGAGAGAAGACAGGTTATTCATTTGTATTCTCTAAGGAGAAAGGATAAAAGGAAAACTGGGTATTTTCTTTTCTATTCTCTTTAGAGCAGCTATAAAGGAAACTAGCAATTTATTTGAATTCTCTGAGGGATTCATGGTTTAATGTGCAAAACATCTGGAGTAATTAAAGGAAAGAAGGTGTGTCCATTGCAGAAAACCACTCTGTAGAATGGCAGGGATTGTATTTTACTTACTTGGCTATTCAGATATGTTTAGAACACTATTTGAAATTCTATGCAAATATTATTGTATTAAATAAAGAATTGGTGTTGATTATATGGAACTAAAAGTTGGCTACAGATTTAAGTAAGAGACTTATAACTTGGACTTTAGTTTTAAGAATAAACAAAATTCTTAAACAATTTTGGGGTCTGCTTATTGAGGACAGGAGGGTCACTCAAGAAACTTCAATCAAAATAACAACTAAGTTGGTACTGCAATTAAACTTCACCTTTCAGCATATTAAAATTAAGTCAAATCCAACCTGGCATTGAACAGTTCCAGGGATGGGATATCCACAACTTCCTTTGACAACCTGTTCTAGTGCCTATAAGGAATAAGGAGTTTATTCCTTATATCGAATCTAAATCTATCCTCTTTTTGATTAGAGTTGTTACCCCTTGTACTATCAGTACTTACCCTTGCAAAATGTCCCTTTCCAGCTTGCTTGTAGGAGCCTTCAGGTCTTCCCAGAGTATTTCTCTTCTTCAGTCTGAACAACCCTAACTCTCAGCCTGTCTTCACAGGAGAGGTGCTCCAGCCATCTTTGTGGTCCTTCTCTCATCTCACTCTAATAGGTCCTTCTTATGTTGGGGACCTTGTAGCTGAACAGTGATTAGAGCACTTGCTGATGAAGACTGAAGAAAAAATGTAATTGAGTACCTCAGCTTTTTCCATATCCCCAGTAATCAGGCTTCCTATTTCCTTCTGGAAAAGGCCTACGTTTTCCCTGTTTTTCCTTTCATCACTGGTGGACCTATAGATTTTCTTTCTGACCTTGACATCCCTGTCCAGTTTTAATTCTGATAGGGCTTTAGCTTTGCTAACATGATCCCTGGCAGCATGGACTATTTCTTGGTATTCTTTCCAGGCTATCTGTCCTTGCTTCCACCCTCTGCAAGTTTCTATTTTGTGTTTGAGCATTTCTTTGTTCATCCAGGCAGGCCTCCTGGTGTTTTTGCCCAACTTCCTTCCATTGCTTAAAGATGGTTCAATTTTGCTGACATTTAAACCAAAATAGAGAAAATACCATGGTGTGAGAATTGGGAAAAATAACAGCTAGCCATTCATTTAATAGATTAAAATATTGGCTTAATTAAGAGAAGAATTTTTGCCTAAAACTTGAACTGAACTTGAACCAGTCCTTCTCGGGGATCTGAGAAATTTGGTTAATGTTTTTCAACCTAGTAAATTTTAATTTTCACATCTCTTCATATTTTAAGCCTGGAATAGGAACAGGAATATTTTGAGAGATAACGCGCTTCTAAAACTTTCAACATTATTGTATAGACCTCTGACATTCATTTCTGTTTTCTGATTTTATTACATTTTAAGAAAATTCCAAATTTAAAAACACGGTTGGAAACTGTGTTATTGAATGATACATATAACATCTCCTTCATCCTCTGTCACTCATATTCATTATTTTTCTGTTTCTGTTTTGTTTCTTTTTGAATACTTTCCTTTTCACTTTCTTTTGACAAACAATATTGAACGTCATGGTTGTAATTCAGACTCGTGGCCATTTATATTGCATTATCTGAGGCTCCCAAATGAGCAGCCTAGCATTTTATGTGAAGATCATGTTTTATTCTATATATAATTCCTAAAAGCTTTTCAAAACAAAAACAAAAATGAAAACAAAAACAAAAAACTGAACAAAACAAACAAACAAAAAAAACCCCAAACCCATGAATAATTGACTGTGAGGGTCTCTGGATTTTCTCAGTATGAGGTGAGATTCATTTTCTGCAAAGCAAACATTATAGTAAACCTACGTTTAAGTTTATGCATATTTGAGTAGCTCATTTGGAACAGAATAAACATTTCTGCTTCAATGGTGCGATACTTTTCAAATATCACAGCTTCTTCTTTAGTATTTAATTAACTAAACCTAGAAAAATACCAAACTAGTACTGACACTGAAGAGGAAAATGCTTCATTTACAATGCTGTAACTTTAATTTGAGATTGTATTTCACATAGATCAGATTTTACTGCAAGGAAGTATCTGCAATTTTTTGCTCTGGGTCTCCATTTCATTACATCAGATTTAAAAGTGGAAGAATACTCAATTAATAGAGTCAACTCTTCACTCATATTCAAGATTCACTGCTGAGGTTCATAATATAGATTATATTTCAAGATTGTTTTTTCTGTGATTCTTCTCATCTCTATTTTGCTCCTATCATTTCAATTCTTTGTTGGCAAATTTCGTCAAGGAAAAGGAAATAAGAATGAACAAAAGACAAAATGAGTGAAGACAGTGTAACACTTCGTCTGCAATTTGTGATTACTGAAGCATGAAATAACGTGATTTTTTCTCTGTGTCTTTAG
Seq C2 exon
ATTGTTTGGCCTGTATCTCATTCCCGAAGGGATGAGTGTAAGTGGGCTGGAAAAGATATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006560:ENSGALT00000042634:4
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
Associated events
Other assemblies
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]