RnoINT0155181 @ rn6
Intron Retention
Gene
ENSRNOG00000048914 | Traf1
Description
TNF receptor-associated factor 1 [Source:RGD Symbol;Acc:1596290]
Coordinates
chr3:14007187-14009052:-
Coord C1 exon
chr3:14008642-14009052
Coord A exon
chr3:14007365-14008641
Coord C2 exon
chr3:14007187-14007364
Length
1277 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGT
5' ss Score
8.1
3' ss Seq
CTAACCAGCCTTCCCTGCAGGTG
3' ss Score
7.72
Exon sequences
Seq C1 exon
GGGAGCCCACAGTCCGTGCAGGAGCATGAGGCCACCTCGCAGTCCTCACACCTGTACCTGCTTCTGGGGGTCCTAAAGGAGTGGAAATCCTCACCAGGTCCCAACCTGGGCTCTGCACCCATGGCACTGGAGCAGAACCTGTCGGAGCTGCAGCTTCAGGAAGCTGTGGAAGTGACAGGGGACCTGGAGGTAGACTGCTACCGGGCACCTTGCTGTGAGAGCCAGGAAGAACTGGCTTTGCAGCACCTCCTGAAGGAGAAGCTGCTGGCTCAGCTGGAGGAGAAGCTGCGTGTGTTCGCGAACATAGTTGCTGTCCTCAACAAGGAAGTGGAGGCTTCCCACCTGGCGCTGGCCGCCTCCATCCACCAGAGTCAGTTGGACCGAGAGCACGTCCTGAACTTGGAGCAGAGG
Seq A exon
GTAGGTGACATGGGTGTATTTTCAGTGTCAGCTCAGGGAGCCCCTCTGCCATCCAGCCTCCTCACCAGTCATCCCTCTCAAAGCAGTTGCCTCCATCCAAGACCATCTCCCCTGTGTACCAGGACCTGCTATTAAGACCCTGAATTGGAAGCTTGGGTTAAAAACCAGAGCCCACTATCCAATGCAAAGCAGGCCCTCTGCTTAGAATTCATTGGGAACCCTTCCTCCATGGCCCCCTCCCTGGCCACTCCATTGCTGACCAGTTGTGATTGCTGTAGAATTCTCTCCACTAAGCCGTGTCTTCCCTCTACTTGTTCCTGGCTGTGCCCCTCAGGGCCTGTGGAACAACCTGCATCCTGTCTCCCACGACTGCTCTGGAACCATAGTCAGTGCTCACACTCTAGCAGACCGATTCCTTCCACGCCTTCGCCTGCGTGGTAGGCGGTGGTGTTCTCTTATTCTCTGCTTCAGTCTCTTTAATACTCCACACACAGACTGTAGCCTCAGACTGACTTGAGTCCGTAGTTCTCAACCCACCTCCTGTATTCAAGACTATTACTTTCCATAATTCAGCCAGCCAGTGCCAGACTCCTGTTACTTTGTTTAAAATAAAAAGCAACATTGCGTCATTGTCTCCCACTTAACCACTCCTGCCTTTAGTTCCACCCCTACTTAAGCTGCTGAGATGTGAGCCGCTCACCTTCTCTCTCATGACTGAAGTTTATTCTTTCAAATTTCTTTGGGTAACCTATTACAGGGTCCAAGCACTGGGCCCAAATGGGCAGGCAAAGCCTCCATCTATACCATTTACACCCTCAGCCCAGTTGAAAAGTACATTCCCTGAGGCCAAGGTGGGTTTCCGTCTCACCAGACTTCTGGCTCCATACCACTGGGTACCATGCAAGATATGAACAGAGAGGAAAGGAGCCCACCAGGGGTGGGAGGGGACAGCCTGGACAGGAGGATGGAAATCATTGTCAGAGCTGTGAAACACGGTGAGGGAGATCAGCCAGCTAAGGGCAATGGCTGGAGACTTCACAGGAAGGGATACATGGGCTGGGCTCCTGCTGGATGACTAAGAGTTGGTGACCAGGGGAGCAAGAAGAGAAAGGGACTCCAAGCATGGGGCAGCATGACAGTACAAATGCAGGCTCAGGCTCTGGATGATGCTTAGACAGGAAAACCTCTCTGGGGTGAATGTATTCCCATGCTCCCCTATCCGAAACAGTCCCCCAACCTGGGTGCTGGTACCTCTGGCTAACCAGCCTTCCCTGCAG
Seq C2 exon
GTGGTGGAGTTACAGCAGACCCTGGCTCAAAAAGACCAGGTTCTGGGCAAACTTGAGCACAGTCTGCGACTCATGGAGGAGGCGTCCTTTGATGGTACTTTCCTGTGGAAGATCACCAATGTCACCAAGCGGTGCCACGAATCAGTGTGTGGCAGGACTGTCAGCCTCTTCTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048914:ENSRNOT00000072400:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.072 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0091721=MATH=PU(15.5=36.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCTGTGGAAGTGACAGGG
R:
GTACCATCAAAGGACGCCTCC
Band lengths:
350-1627
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]