HsaINT0172103 @ hg19
Intron Retention
Gene
ENSG00000124496 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:18273]
Coordinates
chr6:42224701-42225939:-
Coord C1 exon
chr6:42225873-42225939
Coord A exon
chr6:42224841-42225872
Coord C2 exon
chr6:42224701-42224840
Length
1032 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGG
5' ss Score
6.08
3' ss Seq
TTTCTTCTTGTCATTTAAAGACG
3' ss Score
7.11
Exon sequences
Seq C1 exon
ACAGCATCGATGGCAGCAACGTGACGGTCACCCCAGGGCCTGGAGAGCAGACTGTAGATGTTGAACC
Seq A exon
GTAAGGAAAAGTCAATTACTCTTTAGAACAGAAGCCTCAGCTTCTTGAGAAGTATAGTTAATACTTTTGTAGTCAGAGGATTACACTGAGAGAGCAGTTGTAGAAATTGTAGGATCGTGGTTATTTCTTGAGTACTGTTGTTTCCCTGCACAATGGTTGCCAGTATTTCAAGGCCTTTGCCAAAGACTAAATACATGGTCAAAGCATGAAGCCCTGTATTCAGAGAGCCTAGCGTCCCTGCGTCTGGCTCCACAGGCAGTGCTTTCTCATCCCCAGTGACACAGGCATCTCCCTCCGGGTGGCTCATTCTTTAAGAGGCTCCTTCTGAATGTCTTCACTTCCCTCCTCCCCAATTCTTGGCCAGTCCTCCAAATGGGCTTGTTAAGTACTTTAATTTTGCATAGGCAGTGGGTGGTATTAGGAGAGGCAAAGGTGGTTATTTTCATGGATAGGCACAGAAAAGAGGCCAGGTGGTAGAGTGGTGAGTAGATTGAGTCAGGAATCAAAAAACCTAAGTTCCAACACCATTTTGTAATTTGATCTTGATCCAGTTAACCTTTGTAGGGTTTAGTTGACTCGTCAAATGGGAGTAATTATTCCAGCCTTGCTTACATCACAGATCTCTGTGAGGTTCGGATGGGATAATATCTGTGAAAGTGATCTGAAAGAGATAAAAAAATGAATGCTTTGTATTTGTCCCCTTTTTTGTGTTGTTAAATGGCACCATTGGCCATGCTCTGGGAAACTGTTATGTTGGAAATAATCACCCTCCCTCTCCCAGTTACAGGGAGCTGTAAAAGCCCCAGGCCGACTGCCCCCTTGCTCCTAAAATATTTCTCCCTAATCTTAAAGCTGTTCCTTATCCCAGTGAAAAGGCCACGTGTGGAATCTTAGGGTCACACTGTGAGGAAATGCCCCTGCATTCTTGCAGAAAGAACTAGTTTCCTTCTTTTTCAAGTTCCTGACAGTTGCCCTTGGCCTGAGCCATCAAATTGAAGACCACATTGTTGTTTTTCTTCTTGTCATTTAAAG
Seq C2 exon
ACGCATCAACATTGGCTTGAGATTCCAAGCAGAAATCCCTGAACTCCAAGATATCTCTGCCCTGGCCCAGGACACACACAAGGCCACACTGGTATGGAAGCCCTGGCCAGAACTAGAAAACCATGACCTCCAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124496-TRERF1:NM_033502:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.739 A=NA C2=0.023
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0144819=ELM2=PU(78.9=93.8)
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:
ACAGCATCGATGGCAGCAAC
R:
CTCTTTGCTGGAGGTCATGGT
Band lengths:
207-1239
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)