HsaINT0174590 @ hg19
Intron Retention
Gene
ENSG00000125482 | TTF1
Description
transcription termination factor, RNA polymerase I [Source:HGNC Symbol;Acc:12397]
Coordinates
chr9:135273528-135275645:-
Coord C1 exon
chr9:135275422-135275645
Coord A exon
chr9:135273714-135275421
Coord C2 exon
chr9:135273528-135273713
Length
1708 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTGTTCCTTCCCAATTCTAGGTG
3' ss Score
12.26
Exon sequences
Seq C1 exon
GTTAGAACCTGCAAATGAAGAACACAATGTGGAAACAGCTGAAGATTCCGAAATAAGATACTTATCTGCAGATTCAGGAGATGCCGATGATTCAGATGCGGATTTGGGTTCTGCCGTGAAACAGCTTCAGGAGTTCATTCCTAACATCAAGGACAGGGCCACCAGCACAATCAAGCGGATGTACCGGGACGACTTGGAACGGTTTAAGGAATTTAAAGCACAAG
Seq A exon
GTGAGCTTGTGGGGCCTTAGTGTTTGTTGAACTTCCTGTATGCAGAGCTAGCACCTAACTTTCTTTTATGGATGATTCAGATTTATAGATCGACAAGAAGCATTCTTTCTCCTCCTTCACCTCTATCTCCTACCAGAATTGTCCAAGCTGTAAAATTAGCAAAATAAAGTGCACTTGCTTTTCCTCTTCTTGCCCAGTTTCTGGTAAAGGTGGCCAGGAAGAATGGGGCTAAAGAGACCAGATAATTAATTCCCACTAAGAAGAGAAGGGACGAGAGGTTAATTGGTTGAGACACTGGAAATGATACAACAGTTATATAAAATTAAAATGCTGTCAAATTAAAATCAACTTTAATGAGGTATCGTTTCTTTCTCCAAGATATTAAATTGATGGTGAGCCAGTTGTGGTAGACTTGATCACCTTCTTGATTTCACTGTGTTTCTGAACCTCTCTTATTAAGAATTATTATTATTAAGAATAATAAATAACCTTTATTATTCTTAAATCCAATAATAAAGCTTATTGGGTTTAAGAATAAACTGCAAATTTAAGGCTGTATACTACAAATGAGCAATATTTACTGAGTATCTGTTGTGTGAGACCCAATACAACTGGTCATTGAAAAAAGTAAAAAGAGGAGTCATAACCTTCCAGAATTAATGGGATTGAAGAGATTCAGAAAAATAGACAAGACAAATTAAGCAAAAAAGACAGCACTACCCACGTACACACAATTATAGAGTGGTATAGAATCCCATTTTGGTGTATTGTGTTGAAATTTTTATGAGTATGTATTTCATAAAAGACTTTTTTTTTTTTCTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTAGCCCAGGCTGGAGTGCAGTGGCATGATCTCGGCTCACTGCAACCTACGCCTCCTGGGTTCAAGTGGTTCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCTGCCACCAAGCCCAGCTAATTTTTGTATTTTTAGTTGAGATGGGGTTTCACCATATTATTGACCAGGCTGGTCTCAAACTCCTGACCTCATGATTCGCCTGTCTCGGCCTCCCAAAGTGCTGGGATAACATGCATAAGCCACTGTGCCTTGCCCATAAGATATTTTTAAAGTAAACCTAGGCCAAGTGAGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAAGAGAATTGCTTGAGGCCTGGAGTTTAAGACCAGTCTGGGCAAAACAGCAAGACCCCGTCTTACAAAAAATAAAAAATTAGCCAGGTGTCACACACACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAGCCCAGGAGTTCAAGGTTGCAGTGGACTTTGATCATGCCACTGCACTCCAGCCTGGGTGAAAAAGCAAGACCCTATCTCTAAAGAATGCATAAATAAATTTGAAAACTATTTTTTAAAAAGATAGATTAAACAGGAAAGGTCACTTTGGAATAGGATGACCCGGGAAGACATTGACAGAAGAGGTGTGGCTTGGGCTGAACCCTGAAGGAAAGGCCAAATCTGCAAGTGCGGGCAGGAGGGCGAATGTCAGGTGTTGGGACTGTTGGGCCGAGGTACTGTCATTGCTGATGAAAAACCAAGTCATAGGTTTGCTTTTGTCATTATTAACAATACACACTTTCTCCCTGTTCCTTCCCAATTCTAG
Seq C2 exon
GTGTCGCTATTAAATTTGGCAAGTTTTCTGTAAAGGAAAATAAGCAGTTAGAGAAAAATGTGGAAGACTTTCTAGCCCTGACAGGCATTGAGAGTGCAGACAAGCTGCTGTACACGGACAGATATCCTGAGGAAAAATCTGTGATCACCAACTTAAAAAGGAGATACTCGTTTAGATTACACATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000125482-TTF1:NM_007344:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACCTGCAAATGAAGAACACA
R:
ATCTGTCCGTGTACAGCAGCT
Band lengths:
344-2052
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)