BtaINT0152124 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003012 | TRAF1
Description
TNF receptor-associated factor 1 [Source:HGNC Symbol;Acc:HGNC:12031]
Coordinates
chr8:112212176-112214586:-
Coord C1 exon
chr8:112214438-112214586
Coord A exon
chr8:112212261-112214437
Coord C2 exon
chr8:112212176-112212260
Length
2177 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
ATTCGTTCTCGTGTTCCCAGGAA
3' ss Score
9.45
Exon sequences
Seq C1 exon
GACCCCGGGATGGCCTCTGGCTCAGCCAGCAGCCCCCGCCCGGCCCCCGATGAGAACGAGTTCCCCTTTGGGTGCCCCCCCACTGCCTGCCAGGACCCCCCAGAGCCCGGCCCTGTCTGCTGCGCCGTCTGTCTCTCTGAGAAAGTGAG
Seq A exon
GTGAGGGGTCGGAGGAGAAGGGGAGGTTGGGGAGGAGGCGCCAGGGAGGGACTCCTGATGGGAGGCGAGGGCGAGCGGACCCCTGGCTCTCAGGCAGGTGACTGCATCTCTCTGGCCTCGGCTTCCCCGATACCACCCCATCTGACTTCTGGTGGAAGGAGAAGGGGCCACAGAAAGCCCTCAGCTCCCTCTGCTGAAGGCCGTCAAGGGTGGCAGAGCCTCTGAGCCCAGCTGGGCTACTTACTTACTATATGGCCTGTGCGCATGGCTTAATGTCCCAAAACCTCAGCCCCCTTGTCAATAAAATGCCCGTAAAGTGATTTTCTACCTCCCAGGATTGTTACAAGGCCCAATCAGTAACATTTCAAAAGATTCTTATAATAGGGAATTTATCTATAAACTCCTGGGTAAATGACAAACCGCTGGACAGATGTGTCTCCTGCCACAGTATCACCCGTCACCTCAGACTGTGTTGAGAACTCTTCCAAAGGGGACAGAAGTATCTAGTACACTGTTGTATGTTCATGTATTACAGATTTATATATGTGTATATTGTCTTTGTTCAGTTGCTAAGTCATGTCCAACTCTTTGCGACCCCATGGACTGCACCACGCCAGGCTTCCCTGTCCTTCACCATCTCCTATATATTTGTACATAAATGTCTTTATATTTTATATTGTATACAAATATCTTTATATTTCCCTGGTGGCTCAAATGGTAAAGAATCTACCTGCAGTGCAGGAGACCTGGGTTCGATCCCTAGGTCAGGAAGATCCCTTGGAGAAGGGAATGGTGACTCACTCCAATATTCTTGCCTGGAGAATCCCATGGACGGAGGAGCCTGGCGGGCTATGGTCATGGGGTTGCAAAGAGTCAGATGCAATTGAGCAGTGAACGCATCTTTGTATATAATACATGCATTTGGCATATGTATAAAAATATACAATATACACCATATATATTAAAATGTGTATATTATAAATAATTCAAAGAGGTGCGACATCAATATGATCATCAGTATCCCACCTTATTATGCAACTATTATGTACCAACTGTGTGCCAAACACTCCTCAGAAGAGCCTTGGAAAGGTGGACACTGTTATAAGAGGACAGCAAGGCCTAATGGAGAGATGAGGTCAGTTTCCTGGCAGAGGTATTCTTAAATGGCCATGCACCCCCAGCGTGACCTTGCTGGGGACTTTACAGGTTAGGGAGGTGGGAAACTTCTGAGGCAAACTTGAGAAGTTCAAATGCTTTGACAAAGGACAAGGCTAAGAGAAAGACAAGAGAGGTGGTGATGCTGGCAAGGGCAGATGGGGCGGGGAGCAGAGCCTGACTGGTCTTACCATCCTGGGCTCGTCTCAGGCTTTGGCAGTGGGTTTCTTGGTTTCCTTCCCTTTTCTTCCAAAACGTGGTGGGGCGGGGAAGGGTTCCAGGTCTGCCCTGCATCTCTCTACCTCGGCCCACCCCTACGTCCTCTGAGGCCTCGTTCTCCTCCCTGTGAAATGGGCCTGACCGGGGGCGCTCGCTGGGCAACAGATCACTTTACAAAAGCATGTAGGCCCATGTGTCATCGCATCCAGAATCTGACACCCACTCCTGGTTAGGAATCCCAGGCTGGGCGTTCTCGGAGGCCCCTTCTTATTCTGAAAGGCCGGAGTCATCTGTAATTACTAAAAATAAGAGACCAGAATAAAATAGAGGAACCTGCAAAGAACTTATATAGTACACACCCACAATCCCTTAACCGAACCCCTGGGCTCAGATGTATTGAAGAAAAAAACGAAGAAGTTTTTCAGATTTTTGAAAAGCCAGTCAGTACATTACTCTGCCATTCTCCCGGCAGGGACTGGGGACATGCCTTATGTTCAAGCATCAAGCTGTGATATTTCTGCAAACGTAAATATTCATACTAAGTGGGATAAGAAGGGCTTTAACAGCCTAGTCAGTTCAAATCAGGTTCGGCTGCCAGAGAAGCTCACTGCAAGCTATGGGAAGACGTTGGGTGCCCAGTGTTTTTGAGGTGTGGGAATGGTGGGTCTGGGATGGAGCTATATGCTCATGGGTATCAGCTGCCATGCTGGGCAAGGCCCAGGCCTCTGGGGCTCTGGGGATGGAGGTTGGTGTCATGGAGTCTTGAAGGCCTTGCTCAGTGGCATTCGTTCTCGTGTTCCCAG
Seq C2 exon
GAATGACGAGGATCGGATCTGTCCCAAATGCAAAGGGGATGACACCCCATCTGAAAGTCCAGGAAGCCTTCTGTCTCAGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003012:ENSBTAT00000043659:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.532 A=NA C2=0.690
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]