BtaINT0152140 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013475 | TRAF3
Description
TNF receptor-associated factor 3 [Source:HGNC Symbol;Acc:HGNC:12033]
Coordinates
chr21:69228047-69229949:+
Coord C1 exon
chr21:69228047-69228291
Coord A exon
chr21:69228292-69229897
Coord C2 exon
chr21:69229898-69229949
Length
1606 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
TACTGTGTCTCTCCCCTCAGCTC
3' ss Score
10.07
Exon sequences
Seq C1 exon
ATGGAGCCCAGTAAGAAGCTGGACGCGGCCGGCGCCCTGCCTGCCAACCCCCCGCTGAAGCTGCACCCCGAGCGCGGAGCCGGGCCGGCCGTGCTGGTCCCCGAGCAGGGTGGCTACAAGGAGCGCTTCGTCAAGGCCGTGGAGGACAAGTACAAGTGTGAGAAGTGCCGCCTGGTGCTCTGCAGCCCCAAGCAGACGGAGTGCGGGCACCGCTTCTGCGAGACCTGCATGGGCGCCCTGCTCAG
Seq A exon
GTGCGTCTGGCTGGAGGGCCTGGGTCCGGCTGCAGACTTGGGGCGCCCCCCCAACTCCCCCCGCAAGGTCTTTCCCCTGGGGCCCCTGTCCCCTGTCTGCCTGGCCCAGTTTTGCTGGAGGCGCTCACGTTCTGGGGAGGAGCCACCCCGTCCACCAACGATGGTGGGGCCCTTCAGGGCGATCCCCCAGGATAGGGGATGTGCAGCCAGTTCGGGATGTGGGGGGCAGGTCCTCGGTAAGGACAGGACGCCCTGGAGCTGAGTGTCAGGAGTCCGCAGCAGCCCTCGCGGGCACGTCGTTGTGAATTAACGCGTTCAAAGCCCCCAGCGTCAGGGAGGCTGGAGTTGTATAGCAGAGCGTGCTGGTTCATCCCGCAGGTTTCACCCGGCGGGGTGCTGAGCACTGTGCTCAGCCTGGGCCCCCACCAGCGAGTGGGAACCGGGAAGGCTGCCCTGGCTCGTCCAGCCCTCCGCTGGGGGCAGCCTCCCTCCCCAGGGCTCCCTCTGGGGACTTGCGGCTGAGCTCTCGTCCTCTTCCCCCAGACTGAGGACTCAGGTCTGGAACGGAGTTTAGTGGCGCAGCCCCAGGGCGCCTGCTTTCCCTGTGCGGGGCACCGTGGGCCGGGGGCGGGGTCTCTTCCAGTCTCTGCCCTCCTCTGCTCCTGGCGCTCCTCCTGCTCCAGCCTTCGGCAGGTGTCAGGGGATCCTGCCCAGGCGCCCTGGGCTCTAAGGGCGCTCAGAAAGTCCCATGATTAAAACAGGTGAGCACAGGCTCCGTGCTGGTGAAGTCTGGATGAGCGAGCTATCATTTTAAAGCCTGTTAATGTCCCTGCCCCCGACCCTCAGGTCTCCCACCCTCTCCCCAGGGCCCCCCTGCCCACCTGCCTGCTGCTCCCGGATCCCCCACAGTGCCCCTGGCCTGGATGCCAGGTGCTCTCAGGCTGTCGAGGGCAGGGGCCCTGGAAGGAAGGAGCACTCAAAATTAGTTTTTTATTTTTAATCTCTCGGAGGTGGTTTCCAGCACAGGATGGGGGTGAGACTCAAGTCCAAAAAAGGGCAGCTAGGGAGCAGTGGCTCGTGTCCTGAGTTTGGGGACAAGAATCATGTAGGAGACTCGTGGTCTCTGTAGACAGGCTCAGCTTTCGATTCCCACGGGATTCAAGTCCTTGGAATTCCATCAGCCTTTCAGCGGCTGTGAAGGAGACAGCCTGTGAATCCAGCACTTTCTGTGCTGGTAAGGCAGCACTGTTCAGAGGCCCTCCGGGGAGCTGGGGACACTCACGCCACAGAGCCCCTCCGCGCGGAGCTGCTTTTGGTTTCTGAAATGAAATTTCACTTTTAATTGAAAGGGACTTTCCAAGAGGGACTGATCTAAGCTGCTCTGCTGAAAAACTTCCTTATGAAAAATCACTACTAAAAAAGAATCTTAGCCCTTTTCTCCCATTTAAACCGTATTTAAACCAAACTTACCCTGGCATCCTGAAGCCCTGGTGCTCTGAGCTCTGCACAGCAGACACGACCCCTAAGTGAATGGCTCAGTATTCCCAGTGGGTTCAGATGAGAAGGTGCTCACCCTCTAACACGTTTACTGTGTCTCTCCCCTCAG
Seq C2 exon
CTCCTCCAGCCCAAAATGTACTGCTTGTCAAGAAGTCATCATCAAAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013475:ENSBTAT00000017918:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.134 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009720=zf-C3HC4=PU(74.4=35.4)
A:
NA
C2:
PF0009720=zf-C3HC4=PD(23.1=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGCCCAGTAAGAAGCTGG
R:
TGTCTTTGATGATGACTTCTTGACA
Band lengths:
294-1900
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]