RnoINT0155178 @ rn6
Intron Retention
Gene
ENSRNOG00000048914 | Traf1
Description
TNF receptor-associated factor 1 [Source:RGD Symbol;Acc:1596290]
Coordinates
chr3:14017160-14019204:-
Coord C1 exon
chr3:14019009-14019204
Coord A exon
chr3:14017245-14019008
Coord C2 exon
chr3:14017160-14017244
Length
1764 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
ACTTGTTCATGTTTCCCCAGAGA
3' ss Score
8.78
Exon sequences
Seq C1 exon
CCACTCTTTCTACAGACTCCACAGGGCTGGTCTCTACTTTACTTGACAGACTCCTGGCCACCGGAAAGCCCAAGATGGCCTCCAGCTCAGCCCCTGATGAAAACGAGTTTCAATTTGGTTGTCCCCCTGCTCCCAGCCAGGACCCATCGGAGCCCAGAGCTCTCTGCTGCACAGCCTGTCTCTCTGAGAACCTGAG
Seq A exon
GTGAGGGGTCAAAGAGCCGAGGGCCTGTGGGAGAGACTGCTTGGGAGGAACCAGACCCATCGGAGCCCAGAGCTCTCTGCTGCACAGCCTGTCTCTCTGAGAACCTGAGGTGAGGGGTCAAAGAGCCGAGGGCCTGTGGGAGAGACTGCTTGGGAGGAACCAGATGGGATATGGGATTGAAGGAAACAGGTGACTGTGAGGAGGTTAACTTCAACTCTGGGCCTAAATTTCCACACACTTTTCTTCTGAATATTGTCCCTTTCCCCACCTCCCCGGCTGTGGGTGGATGGATCAGTAGCCACAGAAAGCCGTCAGTCAGCCCAACTACTATTAAGGTAGAACTTTTAAGCATCGCTCAACTATCTCTTCCTGCGTGGCCAGGTATGAACCTTGGATGTCTCCAAGCCCCAATGTCCTGCCCGTGGAGTTGTCTTCTGCCTCGCAGAATTGTTATAAGAATCCATCAGTAACATTCCCAGAACTTCTTACAATAATGGTGCCCCCCCTCTCCCCAGCAAATATCAAACTGTGATAAAAAGCACAATTTTGTTTTATTAGACCCAGCTAAAGGGGGCAGAGGTACAGCAGGGTATACATCTGTGCTTAAAGACTAAGTAATTGCACTAACAGCAGCATTGACACCCTGCCCTGAGCACTCCCTATGCATATGCTGTGTGCCGAGTCCCCTGCCCCTGTGCCCTCACACCAGCTTGCAGAGGTCAGTACAGTCCCAGAGATGAGAACTGCAAAGTCTCCCGGAGAGATCAAGTCACCTTGCCTGTGTGAGTTCCCTGGCGAAGATACTCCTAAATGGCCTTGAGCCACGAACAAAATCTTTTCTTTGGGACCTTGCAGTGTAAGAATGTGGGGAAACTGAATCAGTCAAATGGGAAGTCCACATTCGGTGACTAAGGGGAGGAGGCTGCAGGAGCAGGGCCGGAGGTTGTGGCTGTGGAAAGGCTGGGCAGGGGTAGAAGCCACGACTGATGGGCTTCCTGGCCAACTGATGCCCTGAGCTCATATCGGGCTCCCCAAGCCCCACCCCACTGAAAACCTGGCAGAAGAGTGAGCAGGAGCTGACTGGAGTGTGCTGCCAGGGGTCCAGCCTGAGGCGCCCTGCTCTGGATTTGCCTCACTGTCCTATGACCTTGGTTTTATCCCCTAGAGAGCGTTTTGAGCACTTGCTGTCAGTCAGAACTAGGTACCAGGTGTCCCACGGAGCACCGTGGTTCGAATCTGACGCCTATTTCCATTAGACAGACTCTGAGGTCTTTCCTTGTTCTAATAGGCCAAGATCCCCTGCCATGACCAGAAAAAGGAGAGACCAGAACCACATACAGGGTACTGAGAAAAACATGGCGTTCCAAGCCCAGAATCCCTTGACTAATCCCTTGGGATTGGACATATTGGGGGGATTCAAAAGTTTTGCTAATCTGGAAAAGGCAAGTCAGTGCATGAGCCAATTCTTCCAGAAGAGACACTGTAACCAGGTGCTTGCATGGATTATTTCTACAGGGAGACAGCCATAACCACATGGATGAGGAAGGGAAGGCTTGTAGAGCTAGGAAAGCAGCTCACAGCATGCTTCAGGAAACAGTGGAAGCCCAGGGTTTCATAGACCTTGGCAATGTGATTCTAGGATCGAGGAATTACTGCAAGAGGCAAGGTCCGGGCTTTGAAGTCTGTCAGGAAGGTGCGAGTGACCAATGGCAGGTGGCAGCAAGGTATGTGCCTTATTTGAGAGACTTGTTCATGTTTCCCCAG
Seq C2 exon
AGACGATGAGGAACGGATCTGTCCTAAATGCAGAGCAGACGGCCTCCAACCTGTGAGCCCAGGAAGCCTTCTGACTCAGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048914:ENSRNOT00000072400:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.415 A=NA C2=0.207
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCACTCTTTCTACAGACTCCACA
R:
TCTCCTGAGTCAGAAGGCTTCC
Band lengths:
279-2043
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]