HsaINT0172109 @ hg19
Intron Retention
Gene
ENSG00000124496 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:18273]
Coordinates
chr6:42200419-42204149:-
Coord C1 exon
chr6:42203943-42204149
Coord A exon
chr6:42200631-42203942
Coord C2 exon
chr6:42200419-42200630
Length
3312 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
TCACTCCCTTTCTTCCCCAGGTG
3' ss Score
13.12
Exon sequences
Seq C1 exon
ACAAGTGAAGAAGAAGAAGAGTTAGAGGAGGAGGAGGAGGAGGACCCGGAAGAAGATAGGAAATCCACAAAAGAAGAAGAGAGTGAGGTGCCGAAGTCCCCGGAGCCACCACCCGTCCCCGTCCTGGCTCCCACGGAGGGGCCGCCCCTGCAGGCCCTGGGCCAGCCCTCAGGCTCCTTCATCTGTGAAATGCCCAACTGTGGGGCT
Seq A exon
GTAAGTGTGTCTGTGTCGTCTGGGGATCTGGGACAAGTGAGAGCCATATAGCTGTGCCTGGCTTTAAGAGATGATGTATTTTCGAGAGTGCTCTTCCAACAGTCACAGTTTGGCAGAGGGTGCTCCATGTTGCCATTGTTTTCTGCTTCATTTGGCCAACAGGTATTTACAGAGTGTGTGTTCTGTGTCAAGCATGATGCTGCGTGTTGGAGAACACAGAGAAGGCCCCCATGCCCAGGAGTGTGTGATTCCAAGCTCTGCAGTGAGCGTGGCCTCCAAAACATACATTCCACATTTCCTGGAGCCTCTGCATTCCCCTGGGCTGTGTGTCACACAAGCTTGTGCCCTGTCAACATGCATTTAAATGTACTAGGAGAGCCTGCTGACAAAGATCATCCTTTTATGACATAATTACTTGCCCTACCTCCTGCAATTTTACCTATTTAGAAGGTTTTGCATTTCACATTTCATAAAGTGTTACTAATCGAAATGTCACTAATTTAAAATTGAGAACACTGTTACAAAGATTTAACTAAAGTTTATCTTTGTACTCTATGGTGGAGAAAAAAAAGATTTACTAAAAGTAAATTAATCATATAAACAGGCTGAAAGGGAGTGTGTGTAAATACAGAGGCTACTACTTTTCAAGAATATTAGAAGCATAATTTAGCTAAAATAAAACAAGTTCACCATGTGGTCATTCTTAGCACTAAAGAAAGACCTTACGGTATCTGTGCTGGCCTTGTCTAAGGCTCCATATGTATTTTAAAGGATATTTTTAAAGGTTATTTCTCAATCTCCCGCTGGTCTGCCACTAGTCTGAATTGGTGAGCTTTTCCCAAATCAGGTTTCTTAAGGCCAGGCACACCTGTATAGGCAAGTTCTAGAGGGATTACCCCTCAAAATAATGTTGCCCCTTGCAGAGGAAGCCCATTTTCCTTAAGTCAGTGTGCTTGTCTTTGCTCATACATGATATAGGACAGTGCTGTTCTCCAGAGTGTACTGAATGCTGCTTACCTGTCACTTAGATGGAGAAAGCAACAGTCTTTAAAATATTTAGATCCTAAAGCAGAAATTCATTTGATTTGCATTTAAGAAAAAATGAAAATTAAAAAAAAAACAAAAAAGATACATACATTTTGCATTCACTTTGAAGAGAACAGAAGAGATTGCTGGCTTGTTTTCCATCTTTGATGTTTAATGACCTGGCCATTTTGTATAGAGTGTTCACTGCAGCATGATTGCGATAATGACTTTAAGTGATGGTATTTCTTGGTGAATTTGTTCAGAAATTAGATGCCTCCTCAAATCATAGCTCTATGTACAATAAGTTGTGTACCAAATGGAAGTTATCTTTTACTTTTTCCCATCAAATGCTCAGCAAGTTAGATATTTTTCTGTTCCAATTTTTCTGTACATAAGGGAAAAGATATTTTTTAATGACTTTTAAAAATCACAGTGGAAAAAGCGTGCTGGTTTTATTTTATTCCTTGCCTAACGATGGAGGCTTTGGTTGCTAAGTCAGCGATAGGTTTTTTCCTATGTAAGAAAATAACCAGAGCTTGGCCAGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGTGGATCACAAGGTCAAGAGATCAAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTATACTAAAAATACAAAACTTACCTGGGCGTGGTGGTGCGCGCCTGTAGTCCCAGCTACTTGGGAGGCTAAGGCAGGAGAATCGCTTAAACCCAGGAGGCAGAGGTTGCGGTAAACTGAGATCATGCCACTGCACTCCAGCCTGGTGACAGAGTGAGACTCCATCTGAAAAAAAAAAAACAAGCAAACAAACAAACAAAAAAAACAGAGATCATAAACTTAATACAGCAACTACTACAGCTAGACAGCCCAGTAGGTACTCCCCTTAGCTGATGAGTTTAACAAGCTGGAAGCCAGGACTCATTGGATTCAGGGATATGGATTTACACCCCTTTATAGCGGTGGTTCTGAACTGGGGATGATTTATTCCCCAAGAACATTTGGCAGTGTCTGGAATTTATCATAACTTTTATCATAAATGCGGAGGTGCTGCTAGCATCTGGTAGGGCCAGAGATGCTGCTAAACATCCTATACAACAGAGCCCCCCACCCATCACAACAAAGAATTATCCAGCCCAAAATGATAGTAGTGCTGATGTTAAGAAAACCCAGCTTTATGGCAGGATTTTAAAATTCTGCCAAGATCCTTCTTCTTTTTATCATCTGTATTAAAATTTGGGGGTCTTAAACATTGCTTCAACAATGGGCTACTGATTAAGGCTATCTACAACGTAGAATACGTCAGAAAACCTAATCACTGTCTTTCAAACTGGATTCCTTAGGGTGCTAGGGCTTCCTCGGGGTAGATAGAGCTGAGCAAACAGGCGCAATTCTGGGGCACTGTCTCCATTCTAGCCAGAGCACCTCTGCTTTTAACTTGAGCCTGAGTTTTTTTAGTAAGACCTGATTTCCTAAAAAGGAAGGAGGGAGGGAAAGAGGAAGGAAGGAAGAAAAATGGGAGGAAAAGAAGGAGGTAGTTATCATCTTTAAAAAAGTTTGAGGCCAGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCAGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCTGTCTCTACTAAAACTACAAAAAATTAGCCAGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGTGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCTGAGACCGCACCACCACACTCCAGCCTGGGTGACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAGTTTGAAAGCTGGTCCAGCCCTCTCATTCCTCAGATGGAAAAAAATAAAGTATACAGAAGGGAAATGGCCCAACAGCTTTAGTTATAGTAGAGCTGGGTCCAAACCCCTGACGTCTTGACTTCTAGACAGTAGCTTTATTCTTTATCCTGTGCCACGTCGCTTCTTCTCTTCTGATTGTAGCAGTGATGAGGTTTTGATTGGCACAGGATCTGTGGTTGTGGTATTTGATCTTTACCTTTTGTAGCATATGCCCAAAGTTTGCTTATATAAAACCCTTGTGCCCTGTCATTAGACAGTTTCAAGTATTCCATGTTTACCACTGAGTAACTAATAACCCTAATTTCCTTTTCAGGACTGTAGATGTCATGTCACTCCCTTTCTTCCCCAG
Seq C2 exon
GTGTTCAGCTCCCGACAGGCACTGAATGGCCATGCCCGCATCCACGGGGGCACCAACCAGGTGACCAAGGCCCGAGGTGCCATCCCCTCTGGGAAGCAGAAGCCTGGTGGCACCCAGAGTGGGTACTGTTCGGTAAAGAGCTCACCCTCTCACAGCACCACCAGCGGCGAGACAGACCCCACCACCATCTTCCCCTGCAAGGAGTGTGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124496-TRERF1:NM_033502:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.783 A=NA C2=0.819
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)