RnoINT0133046 @ rn6
Intron Retention
Gene
ENSRNOG00000004033 | Sema6a
Description
semaphorin 6A [Source:RGD Symbol;Acc:1305493]
Coordinates
chr18:41363666-41365983:-
Coord C1 exon
chr18:41365903-41365983
Coord A exon
chr18:41363725-41365902
Coord C2 exon
chr18:41363666-41363724
Length
2178 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CGCCCCCGCCCCTTTTAAAGACT
3' ss Score
6.3
Exon sequences
Seq C1 exon
AACCTGTATCGCCTCCAGAGACCCATATTGTGGGTGGGTAAAGGAAACTGGTTCCTGTGCCCATCTGTCACCCCTTAGCAG
Seq A exon
GTAAGGAACCTGAGGTGTGGGAGGGCAAAGTGCCTCCGTTACTCTTCATGCTAGATGTAGGCTTGCCTGTGTTCCCTCCAACCATCTGTACTCACTTTTCTCTGTGAGAAAAATTCAGCCATGGTACTGCCAGGTGGCTCCTCCTCCATCCCTACTCAGTTCATAGCCTCTGCCTCATCCCTGGCAGAGTGTCCATGGAATAATCACCCTCAGACTGGTTAAGAATGCAGAAAGGAAACACAGTAGGCTTCAAAAGTATTCCCTAGAAAGTGGGACAGGAAGATGCCCGCCTTGAACATCACAGGTAGAGGATAGCAGAGAAAGAAGCCATGGGGAACCAACTAGATTAGTTTGTGCAGCCACAACAAAATGAGTTTGCTAATTGACCAACCGTCCAAGGCTGAGAAGAAATAGCAGAGCATTTGTTAACCCATGTGATCATGCGTCAAGCATGGTGTTCATATCCAATAAAGCTTTCTCCTATGCTCAACTAACCCTGACCTCACTGTTCATTCGGCACATAATCAATGTTTGGCAATTTCCCAATTGGTCCCCGAGATCAAGCCTTTATCTGTTCTGCCTGTGAGGTTTTTTTTTTTTTTTTTTTTTTTTTCCACTTCATAGGTTGTGAAATCTAAAGTAACATTTGGAAAAAATATTCAAAGCATGTCTCAGAGAGATGGTGGATAATGCAAGTGAGGTATCCAGGGCAGTCCAGGGCTCTCCCTCAACAAAGGAGCTTCCCCGGGACCATCTGTAAAACAGAACTACTTTCCTATGCTGGGAGCATCTTTTCCGCTTTGAAAATAGCTAGACAACTAGAAAGAGACAATTTAGTGATGACTGCCACCCACCTATTCTCTTGAACGGAGCTAATGATAACTGTAAAATATGACCTGGAAACCTGAGCGCTGCAAAGCTAACCCACTCTGTATTATGAGCGTGGCTTTGCAGGTAGCACTGTTGCCTTTTGATAGTGTTGGAGCCTTGTATCTTTTCACTGGGGTAGGACAGAAAGAATCAGTGAGATGGGGAGCCGAGAAGGGGCTCATCATTTGTCAACAAGTGGACAAAGATAACAAGACGTTCATAAGCAGTTTTCACGTCATTATCAGGACTCCCAGAGGAGTCCTGTAAGCCCTGCATTTATCTTTCAGAGACACTGCCATTGCTCAACACATGAGTAGTTCTGCTGTGAGAGTGGGTTTGGGGACTGGATAGATACTGGCTTTCATTACAAGAAACCGTATCCTTAGAGAATGAATTTAATTTTCATTACAGCGAAAGATATTAGAGGCTAAACATGGATTATTAGATCAAGGTGTGCCTTTCCAAAGTGGTTTCTTACATGGTTCATGATAAACTGGGAGACAGTCCCAAATCAGAATTTTCAATTACATTTTAGAAACATAAGTGCAGAGTGGACAAATCTGGGTGTGCTTGTTTTCAATTTAAATTTTTTTTTTTTGGTTTTTTTTTTCGGAGCTGGGAATCGAACCCAGGGCCTTGCGCTTCCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCATGGGTGTGCTTGTTTTAAAAATTAAAGTAAGTATGTGGTGACCCAGAGGATGGAGGAGGAAGAAGAAAGGAGAGTTGATTATTGGACTGGGGGAAAGCAAGATCCTTGCTAGAGTCCGCCCTCTCGGAGCCTGCACATGCTCACTGGCCAGTTGTGCCTTTAAACACTTGGTTATATGTGCTTTGTAGGCAAAGAAATAGAGAAAGGGACCTGGGAAAGCAAGGAGAGGAGTAGGAAAGGAATCAGAAAGAACAGACACTTTCATCCAGACTTCCCATGTTGCTTATATGAGGAGTAGCATGAAAACTTTTTAAATGTTTAAGTAATGCTCTAGGAACCGGAGTAAGGACAGCAGAAGAGTAACCCATAAGCTAGTTAACTTCCTGATTCAGCTCTGAGCTCACTGCTATCATAGCTACCTTCTCTTTGGAGACCCCCTCAAACTCACTGTTATAAAGCTTCCGAGAGCTGTTTCTCTCTTATGCCTACCGCTTGGCTTAGCAAAAGGGTCACTTTTTTAATGAAACTAAAGACTCACTGATGGCATTGCATTTTTTTCTCTTTCCTTGTCTCTTCCCCACCCCGGCCCCCGCCCCCGCCCCCGCCCCCGCCCCTTTTAAAG
Seq C2 exon
ACTGGCTTTTGAGCAAGACATAGAGCGTGGCAATACAGACGGCCTAGGAGACTGTCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004033:ENSRNOT00000005446:14
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:
PF0143720=PSI=FE(40.9=100)
A:
NA
C2:
PF0143720=PSI=FE(30.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
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]