HsaINT0171669 @ hg38
Intron Retention
Gene
ENSG00000056558 | TRAF1
Description
TNF receptor associated factor 1 [Source:HGNC Symbol;Acc:HGNC:12031]
Coordinates
chr9:120925936-120928769:-
Coord C1 exon
chr9:120926550-120928769
Coord A exon
chr9:120926302-120926549
Coord C2 exon
chr9:120925936-120926301
Length
248 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATGACTGGACACTCCTAAAGCCT
3' ss Score
-0.56
Exon sequences
Seq C1 exon
GCGGCGGGGGCTGTGCTGGCGCCGGCAGGCGCGAGGAATCACAGAGCGGGGCGCCCAGCCTCATCATGGGGCGGCCCACGGAGACTTCCCGTGGGAGTGGGGTCTGGTGCAGGGGCGCCCCAAAGGACGAGTGGGAGATGGGGACACGCGGCGCAGAGAGACTCCTCGTGGATGGAGCCGATGGAGGCCCAGTGTAGAAGAGAAAGGGGTCAAGGAGACGGATAAGGAGCCACCAGAGACGCGGGGGGAATTCCCCGCAGAGGATGCGGGAAGCCGGGGAAAGGAAGGGATTCCGGAAGGAAGGGCTGAGAGCCGGGTCAGGTGCTGGCAGGAGGGCTGGTTGGATAGAAACTGGGGCGGGCCCAGGGCATTTGGCGTCCCCGACATGCGTATACACTTGGAGAGATGATTCCCTGGAGATCCAAGTGCCTGTATAGACAATCTTTTCTAGAAGTTCTACCGTTAGGTGAGGCGAGAGTAGATGTAGAAATTGGAGACGAGAATAAAGAGTGTTTTAAAAGCGTGCGTGGTTACAGGACTGGCTCTGGGTTCAGGGGTCCCCACTCACTAGCTGTGAGACCTTGAACAAGTCGCTTAGCCTCTCTGTGCCTCAGTTTTCTCATCTGTAAGGTGGGGATGATGATGGCAATACCTGCTTCACAGAGTGAAAATTAGATGAGATGATGTCTGTAAAATTACGTAAGACGGTACCCAAAAGTAGTACTATTTTTCCCTTTTCTTATTAGAGCAGGTTGCGCACGTTTTGATGTCCGTGGGAATGAGCAGGTAGAGAGGGTGGTATTGAGGCCGGAGGGGAGAGAAGGGACCCACAGATGGGGAGAGAAGTCTTGGGTGCCTGTTTTATCCCAAACCAGGGGAAGGAGGGAACAGGTAGGGCTGGCTGCAGGAAAGCTTGCAGGTATGGGGTACACAGTTAAAAGGGAGTGTCTTCTGATAGTCTTGATGCAGGCCTGGAGGTCGTTTGTTATGGGGGTGGAGGTCCTGATGTACATTGTGGCGGTAAGATGCCGTGCTGTCTTTGCCACCAGCCTGTGGCAGCCCTGGTGTTACACCAGGGCAGGTGGGCAGTTTAATGTATCTCAGGCCAGATGACCTGCCCTGCCCACCTGTTGAGGCTCCAGTAGATAGACGTGAAAGCACAGTATAAGCATAATGCACCACTTTAATCCTTTTCTCTGAGGAGCTGGAAGGCCTGTAGTCACCATCTGAGCCAAATGTCATTCAAGTACTTCACTTGGGTTACACACCACACTTTGACCCACTATCTCATTTAGTCATCACAACAAATGGGTGAAATAGGTATTATTGTCCCATTTTACAGATGCAGAATCTGAGTTTCAGGGAAGTTAAGGACTTTGTCCCAGGGCCCACAGTTAGTAAGCAGTGGACCCAGGATTTCAACTCAGCTCTGTCTGACCTCAAAACCCATGATCTGAAACCACTGTGAAAGTTTGCAAAACCTCTGTAGCAGCCAAGCAGGATGGAAAGATGTGTAGGGATTGTCTTCTCCATTTGATAGATGAGACAAGAGCTGGGTACTCTGATCTCCATCCCAAGCACACAGAGCTTGGGGCCCCACAGCCCTGGTGTGAATCCCACTCCACTACCAGAGGCTGTGTGCCTTTGGACCAGGCATCTTGCTTCTCTGACCCTATATACAGCTGCAGAAGAATTCCTTGCAGGTTGCTGTAAGGATTTGGAGGGAAACTGTTGCCCAGCACACAGTACACATTCTGGGAGCCATCGTTTCCCCAGTGCACTTTTCCTGCAAATGTGGATCTACATCCCACTTGGATGCTGAGACCAGCTGCTGTGATCTTGCATTTGTTTAGCGCTTTGTTCTCCTTGAGGCAGTAAAGTGGTGGCACCTGACCGGAGCATGTAGCCACCTATGACTTCCTGAGTGGGGTGGTGTGGGGAGGGCCCTGAGGAGTCTGTGGTCCTAGGCCTTGGATTTCATCAGGGCTTTCCTGCTCCTTCTGGTTGCCTCAGTCCCAGGCAAGATAGGGTCCCAGAATCTTACAGCCCAGAGGCCACCTGTTGCAACTTCTTTTTTACAGATGGAGTCATCAGAACCCACTGTGAGGAAGTGACTTCTCCTTGAGGTCACCCAGACACTCCAAACAGAGCAGAGCAAAAGCGCCTAGAACTTGAAATTTTGGACCTGTCTCCAACACCCTGGGGATTTCCACCAGGAAG
Seq A exon
GTGAGCACCCCCACTGAGAATTCCAGGCTGCTCAGAGGTGCCAGGGAACACAGACCAGGGACCAGCTGTGGCCCCCTCCTCCGATGTGCCCAGGGAAGTGGGGGAAGCCAGCGGCAGCCTGCGATTCTCAACCAGGGGAACTCTCACTGTGCTTTCTGAGAGTCTGTGACACGGGTCATTTTCTCTGACTTGCTCTCTTGCTTTTTCTCACTCTAAAAAAAAAAAAAAATGACTGGACACTCCTAAAG
Seq C2 exon
CCTTCAGTCACCATCCAGGGGATTTTTATCGCCACAAAGGGTAATTCCTGCTCCATCCCTGCTGTGACTCAGCTGTGACGTTGAACCACACAAGCCAGAGAGAAGAAGATAAAGTCATCAGAGCTCCTACTCACCAGAGAGTGAGGCCCAGGCCAGGACTCCACAAGGCTGGTCCCCTGCCCTGGAGCAACTTAAACAGGCCCTCTGGCCAGCCTGGAACCCTGAGATGGCCTCCAGCTCAGGCAGCAGTCCTCGCCCGGCCCCTGATGAGAATGAGTTTCCCTTTGGGTGCCCTCCCACCGTCTGCCAGGACCCAAAGGAGCCCAGGGCTCTCTGCTGTGCAGGCTGTCTCTCTGAGAACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000056558:ENST00000373887:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.372
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCCCAGGCAAGATAGGGTC
R:
GTGGTTCAACGTCACAGCTGA
Band lengths:
298-546
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains