GgaINT0061027 @ galGal4
Intron Retention
Gene
ENSGALG00000002294 | SEMA6A
Description
Semaphorin-6A isoform4 [Source:UniProtKB/TrEMBL;Acc:E1C1C2]
Coordinates
chrZ:72453600-72454795:+
Coord C1 exon
chrZ:72453600-72453688
Coord A exon
chrZ:72453689-72454577
Coord C2 exon
chrZ:72454578-72454795
Length
889 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TCTTGCCATACTCCTTCCAGGTA
3' ss Score
9.86
Exon sequences
Seq C1 exon
AACCATACTTTGTCCAGGCAGTGGACTACGGCAATTATATTTACTTCTTCTTCCGGGAAATAGCAGTGGAGTACAACAGCATGGGAAAG
Seq A exon
GTAAGGGCAAAAACATTGCCTCAGATGACTTAGTGACATTCAGGAGGAGAAAAACATATGCTATTCTTGGACCGGTGCAATTAGGAATGACCTTGAAATGAAAACCATAAATCACGATGACAAGGTCATCATTTTGAGAAGCTTCGTATCACTCAAGCCAAAAGGTGGGCTGGAGGGAAATGTTCCACTGTCTTGAAGGGAAACAGGGTGGTTTCTCACAGTGGTGACTTACGCTGGAATCTCTTTTCCCAATGATAAAAAGCACAAGGCAAATGTAGTACATTCAGCGTGCTAGACAGTCCTTTAAAATGGCTTCTAAAGCAAGGCATTATTTGTCTTTAAGAAATCTGAATTTCAGTAATCAAGGGGAGAAATTTTGTGCTCTGCCATTCTTGAAAGAATAATTAAACATTTACTGCATTTTTGTGAATTTCACAATAGTTTTTCTGACTAAGCAGTCAGAGAAACTGACCAAGGTCAGAAAGGTGGAGGGCAGGAATAAAAGCCCAGCAAAATTTGCATAGTTTTTAAGTGCTGAAAATACAAGAGTCAGAGCAGGCAGTGTGGGTTGCAGAGACTGAATATAAAATGTGCTATTGTTTGGGGAAATAGAAAGCTAAGCAGTCTGTATGGAAATGAGTTTTATTTGGGTTGAGAACAGATCTCTTGAAGGATTTATGGCTGTGTATTAAATGCCACAGCCTTATCATCTATAACACGCTGTTCCAAAGCTGAATTTTTCTCAGTTTCTTATTGTCACAGATTATGGAAACATGGGATTAAATTAAGCACCTTGCTGTGTCGTTTCAAATGTTTTAAATGCAGAATTCCTGTAGTCTTTGAGTTAAACATTTCATTTTCTCTAATATTCTTGCCATACTCCTTCCAG
Seq C2 exon
GTAGTTTTCCCGAGGGTGGCTCAGGTTTGCAAAAATGATATGGGAGGATCTCAGAGAGTGCTGGAAAAACAGTGGACTTCCTTCCTCAAGGCTCGTTTGAACTGCTCAGTTCCTGGCGATTCACACTTCTACTTCAACATACTGCAGGCAGTTACAGATGTTATCCATTTCAATGGCCGGGATGTTGTTTTAGCAACCTTCTCCACTCCATATAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002294:ENSGALT00000003608:9
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(6.7=100)
A:
NA
C2:
PF0140314=Sema=FE(16.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCATACTTTGTCCAGGCAGTG
R:
ATATGGAGTGGAGAAGGTTGCT
Band lengths:
302-1191
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]