GgaINT1028419 @ galGal4
Intron Retention
Gene
ENSGALG00000009864 | TRAF-5
Description
TNF receptor-associated factor 5 [Source:RefSeq peptide;Acc:NP_989550]
Coordinates
chr3:21614250-21616292:-
Coord C1 exon
chr3:21616071-21616292
Coord A exon
chr3:21614308-21616070
Coord C2 exon
chr3:21614250-21614307
Length
1763 bp
Sequences
Splice sites
5' ss Seq
GCGGTTAGT
5' ss Score
5.46
3' ss Seq
CAACTCTCCTTTTAATCTAGAGG
3' ss Score
5.37
Exon sequences
Seq C1 exon
GGCTTCCATGGCCTGTGACGAGCTCACTGGTGTCTCGGGCATCTTTACGCGCCAAAACTCTGCTAGTGCTGTTTCTCTGGACTTCGAACCCGACACTGACTACAAGTTTGTGGAAACCTTAGAAGACCGGTACAAGTGTGCCTACTGCCATTCAGTCCTTCACAATCCCCACCAGACAGGATGTGGGCACCGATTTTGCCAGCAGTGCATTCTCACTTTGCG
Seq A exon
GTTAGTACAAACTCCTTCCTGTATCTACAGGCTCCCCGTCCTCCTGTTCTTAAACAGAAATCAGCACCTTCCATAAATCAACAGTAAATTCCATAGTAACAGTGACTGGTAACACATTGTATGGGAGTCAGTGGGAAGACTTCTGAACTCAATGACTGCGTGCTCAGTCTTTTAAAGGTGTCTTTAAAGATCTTACAGGGCGCTGCTGAGAAATATAGGATTGCTTTGGCAACTGCAGAGAAGTCAGCATATGAAAAATTTTTATATAAACTGAAACATTATTGAGTGGGACAATGTCTTGGTTTGTCCATCTGTTATTGGTACTACTCAAGTGATTTTTTTTGGTTTTTTGTTTTTTTGGTTTTTTTTTTGCATTAATATTTCATGTTATTGGTACCAGTGGCTAAATTAAGGCTAGTTTCATTTGGTTCCATGTAACTTCTTTTCTTGCAGTGGAGTTCTTGACCTGATGTTAGTATTACCCAAGACTACAGTGAGATCAGAGGGCTGCTGCCATCCGTTTGCTTGGGATTCACCTGCAGGTGTAAATAAGGTTACCCTGCAGACCTATCAAATATTTTGTGTGCGTGTGGGTAGGATTCTGCCCAGAATGACAGCAGAGAAGCTGGATTGTGTAGATAGATGTTGCTTTTAATTTTTATGAATGTTAGATGATTTATGTTTGTCACTTTTCCCCCTCTGGGTTGCCTCCCTTTGCTCAATTGCCTCAATATGCATTTTCTCATCTTTTATCATAGGACTACTTTTAATACAGGGGCAATTAGGTCTTCCTTTATTGTCATAACAAGGAGTGCACTGCTTGTAGTAAACAGAGGCTTGGCTTAATGCACGCAAGGAGATTTTTTCAGATATGACAGTTATGAGAAGCAGATGGCCAGAGAGTGACAAGATCTCCTTTAATTTAAAAGGCATCTTATTAACAGTTGTAGGATGAACTGCTTTCTGTTATTAGTTCACTGCCGTAGCTTAATAACCTCTCAGAGCTCTAAGCAGACTGTGGCTGTGTAGCTGCTAGATCAAAGCCTTTTCAAAATGCTTTTTGATTCTTATGGTACCCCGGGTGAATGGGACGTAGACAAGTCACATTCCTTCCACACTTTATTATTAGATAAGTTCTAGGTATGATGTTTTGTTGATTCATACCAAGGAAAATATCACTTTGACATAGGAACAGCAGATAAGATTTAGCTTGCTAAACCATCTCCAACTTAAATTACTTATTATAAAAGTGACTAAAATGTAGGAAATTTAAGATGGATCAAGAATAAGTGCCCTCAAACTATTCAGGCTGGACTTTCTATTAATGAACCCATACTGACTATGCCTGATAACAGCTTTGTTCTTTAAGTGCCTTTCCATATCCCTCAGGACAATCTCCACAGCTTTTCCAGGTTAGGTCAACAGGTCTGTGGTTTCCCAGGTCTTCACCTCCTTCCCTGTTTGCAGCTGAGTATAATACTGTGCAGATTCCAGCCAACAGAAGGCTTCCCATACCCTCATGACCTTCATTAGATTGTTGAGAGGGGTTCAGCTACAATGCCCACCTCGGTGCCCTGGAGAGATGCTATCAGGGTCCATGGACTTCTGAACATTCAGCTGATAGAGCTGTCCCTTACAATTTTGGTGACCACAAATTTAAAGTCACTGCTCCATCACCCATGCCAGTTGGATTCTAGTGTAACCCAATCTTGGAAAGTAAATCAAATGTTCTGTGGGTTAACACAACTCTCCTTTTAATCTAG
Seq C2 exon
AGGACTGAATGCAGTACCCACCTGTCCTGTCGACAAAGAAACAATAAAAATGCACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009864:ENSGALT00000016038:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139231=zf-C3HC4_2=PU(70.0=38.9)
A:
NA
C2:
PF139231=zf-C3HC4_2=PD(27.5=55.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTTCCATGGCCTGTGAC
R:
CGTGCATTTTTATTGTTTCTTTGTCG
Band lengths:
278-2041
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]