HsaINT0172118 @ hg19
Intron Retention
Gene
ENSG00000124496 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:18273]
Coordinates
chr6:42225873-42227461:-
Coord C1 exon
chr6:42227077-42227461
Coord A exon
chr6:42225940-42227076
Coord C2 exon
chr6:42225873-42225939
Length
1137 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTCTGATTTTTGTGTTTTAGACA
3' ss Score
9.52
Exon sequences
Seq C1 exon
GAAATCCCCAGGAAGCATCAGCCGAGTGTGCCCAAAGCCGAGGAGCCCCTCAAGACCGTGCAGGAGAAGAAAAAGTTCCGGCACCGGCCGGAACCTCTCTTCATCCCGCCGCCGCCCTCCTACAACCCGAACCCCGCTGCCTCCTACTCGGGCGCCACCCTGTACCAGAGCCAGCTGCGCTCCCCGCGCGTCCTCGGGGACCACCTGCTCCTGGACCCCACCCACGAGCTGCCCCCTTACACGCCCCCACCCATGCTGAGCCCGGTGCGCCAGGGCTCGGGGCTCTTCAGCAATGTCCTCATCTCCGGCCACGGCCCTGGCGCCCACCCGCAGCTGCCCCTGACGCCCCTGACGCCCACACCACGGGTGCTGCTGTGTCGCTCCA
Seq A exon
GTGAGTCACCCCTTTAGCGTCCTCCTGGGCTCTGGGTGCTGGGTAAAGTCCTGGGACATCTCGTTTTCTTTAGCTTTCTCATTTATCCCACAGACTTTTGCGGAGTATTGGCTGTATGTAGCACGCGCTGCTGGGTGTTAAGAAAGACTTGGAATACATAGCCCTTATCCTCAAGGGAATCGCAGTCTAATTGGGAGACAGATGCATAAAGTGATCACTACAGTCTCTGGGATAAGGAAACAGTTGAAATGTTCACCCACTTTTTAAGGCTGCCAGCAATGATCGTGCAAGAGAGAAAAAATGAGACCGGGCGCGGTGGCTCACACCTGTAATCCCAGCGTTTTCGGAGGTCGAGGCGGGTGGATCACTTGAGGCCGGGAGTTGGACACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCATGGTGGCACGCACCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGGAGAATCGCTTAAACCTGGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCTAGCCTGGGGGATGAGAGTGAAACTCCGTCTCAAAAAAAAAAATAACGGGATGTGGTAGCAGGCACCTGTAGTTCCAGCTACTCAGGAGACTGAGGCAGGAGAATCTCTTGAACCCGGGAAGCGGAGGCTGCAGTGAGCCGACATCGCGCCACAGCACTCCCGCCTGGGCGAAGGAGCGAGACTCCGTCTCAAAAAAAAGAAAATGTACTCAGTAGATGTACAAATAAGATTAGGTATTACATGCAAGATCAAGCCTTGACATTTTAGCATGCTTTATAAAAATCAAGCATAGAGAGGCTAGGATCTCTTTCTGGAGCAAGAATAATTGCATAGAAATCATACCGCTTAGCAGACCATTGTGGGACAGCTGGCTTCTCCTCACCCTGTGTGAGAAATGGGTAACCCTAAGTTATTTTGCACCATACTCCACCCAGCTCCCTGGAAACTGTCAAGGATAACTCTGGCAGGAGCTGGGTAGGAGAGAAGCTCTATTATGGCTGGTTAGGTAACTGCTCATTTGCTTTAGTCTTTTTCAACATTCCTTCCCTGTTGACTAGTGACCTCTGATTTTTGTGTTTTAG
Seq C2 exon
ACAGCATCGATGGCAGCAACGTGACGGTCACCCCAGGGCCTGGAGAGCAGACTGTAGATGTTGAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124496-TRERF1:NM_033502:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.809 A=NA C2=0.739
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGAACCTCTCTTCATCCCG
R:
TCTACAGTCTGCTCTCCAGGC
Band lengths:
356-1493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)