BtaINT0152137 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010497 | TRAF2
Description
TNF receptor-associated factor 2 [Source:HGNC Symbol;Acc:HGNC:12032]
Coordinates
chr11:106298272-106299943:-
Coord C1 exon
chr11:106299869-106299943
Coord A exon
chr11:106298599-106299868
Coord C2 exon
chr11:106298272-106298598
Length
1270 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GAGCGCTGTCGCCCCGGCAGGTG
3' ss Score
7.73
Exon sequences
Seq C1 exon
TTTCAGGACCACGTCCGGGCGTGTGGCAGATGCCGAGTCCCATGCCGATTCCACGCTGTTGGCTGCCCCGAGATG
Seq A exon
GTGAGTCCGGGTCTGCAGGTGGCCCGGGTCCTCGTTCTCAAGCAGAGACCCTCCTGGACACGTCTCCACTCTCACTCCAGCCCGGCCCACGGGTGTCTGGCTCTGTCCATTGTCCTCCCAGTGATCCCCAGTGCCCAGCCTTGACCACCCAGTGGAAAGGATGCCCAGCATGTTGCGCCCCCCGAGGGCTGGCCACGCCCCCTGCCCATCCGCTCACCTCGCTTCACCTGGCTATTCTGGCCAAAAGCCCCATGGTCATCCTGGACCTGCCTCCTGTCTCTCGTCACGTCCAGTCTCCAGCCCAGCTTCTGTTCTTCCCAGACGGCCCCTAGCCCTCCCCACCTCACTTCTGTGGCCTGCGTGGCCCTGCTGTGTGATCTCAGTCCAGCCACTGGCCCAGCTGTCCTCCAGCACGCCAACTTTCTCTGGACCTTGAACCCACCTCCTCTCTGTGGCCGCTCCTGCCAGCTTCTGGGCGGCTCCCTGTGCGTGTGGCCCTGGCCCTCCTCTCTCACTGGTTCTGTGTCCCTGAGGGCTGGGCATGTGCAGGCCTGGCCCGTAGAGATGGGCACCCCAGCCCTCTGCACTCGGCGGGCGCGGCCTGCTGGCGCCGCTGGTACCTGGTGACTTGGCGTCACCGGGTCTCAGCACCTGCCCTGATTTTCTGAGGTTGAATGGGGGTGGGGCCCCCTCCATCCCTCGGTCTGTGTGTGCCCTCCTGCTTCTGGGCATTGCAGCGCTGGTTATTTCCCACATGGGCCCAAGGGCTGTTAGCGGCCAGCAGAGGGGCCCAGGGCATGAAGGGCCTCTTCTCAGCCTATGGAGGGTCCGGTCCTGTTGACCTCGTGGCTCCAGCAGCAGCCTCGGCGCAGCCCCCACGTCAAGCGCCCCAGGTTCCCGGGCACGAGGCCTCCCCTGCAGCTGCGTCCCTTTATCTGTGCTCTAGACTTTCTCGGCCCTTTTGACCCTCCACACTCGCTGTGGAGCTTTGCAAGGGACGTGGCTGCAAAGTCAGATCTGTGCGGGGGGACTACCTGAAGGTGAATTTTATCCCCACCCCCTGCCGTGTGGCAGTGTCTTTGATGGCTCCTCCCGCGGCTCACACGCGGGGGCGGCCCGTGGGGAGGTCTGTGTCCCAAGGTGGGGGTGGGTGGTACCGCGCTGCCGCTCAGTGTCAGGACTCACCCTCCTGCCACCACGCGCTTGGGCACCGGCGCCTGCTAAGGTCTGCACCCGGGGCCTGCAGGGCTGAGCGCTGTCGCCCCGGCAG
Seq C2 exon
GTGGAGAGCGAGCAGCAGCCGGAGCACGAGGCGCAGCGGCTCCAGGAGCACCTGGCCCTGCTGCTGGGCGTCCTGCTGGAGGCTGGGCGGCCCCCGGGGGACAGCCGCCTGCTCCTCAGGCCAGGCGAGGGCGCCTTGGAGGCCGGCACACCCTCCAGGGTGGCGGAGCTGCTGCAGAGGTGCGAGGCCCTGGAGCGGAAGACAGCCACCTTCGAGAACATCGTCTGTGTGCTGAACCGGGAGGTGGAGCGGGTGGCCGTGACGGCTGAGGCCTGCGGCCGGCAGCACCGGCTGGACCAAGACAGGATCGAGGCCCTGAGCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010497:ENSBTAT00000013869:7
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=0.138
Domain overlap (PFAM):
C1:
PF0217613=zf-TRAF=FE(41.4=100)
A:
NA
C2:
PF0217613=zf-TRAF=PD(13.8=7.3)
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:
GAGTCCCATGCCGATTCCAC
R:
CCTCGATCCTGTCTTGGTCCA
Band lengths:
354-1624
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development