HsaINT0073579 @ hg19
Intron Retention
Gene
ENSG00000170627 | GTSF1
Description
gametocyte specific factor 1 [Source:HGNC Symbol;Acc:26565]
Coordinates
chr12:54856955-54858951:-
Coord C1 exon
chr12:54858851-54858951
Coord A exon
chr12:54857082-54858850
Coord C2 exon
chr12:54856955-54857081
Length
1769 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
CCTTAATTTTGGTTCCACAGAAT
3' ss Score
7.99
Exon sequences
Seq C1 exon
CCGACTCCCTGGACCCTGAGAAGCTATTGCAATGCCCCTATGACAAAAACCATCAAATCAGGGCTTGCAGGTTTCCTTATCATCTTATCAAGTGCAGAAAG
Seq A exon
GTAGGGTCATAATTTGCCCTCTAACACCCTCCTGAGTTCTTTTAAAAGGCCATATTTTATAAATATCAAATAATTTTATCATGTTTTAATTGATTGCCAGAATTGTTTTGGGAATCTACCTCTCTTAAATACCAACATTTATAGAAAGGCATTTGTTCATTCCTTAGGATAAATTTTTTCTTGTTTTGGTTTTCTTCCCATTAACTAGTGACAAAGAACCCTTTATAAACAGCATCTCTAGAGTCTTCTCACCCTTTGTAAAACAGACTAATTTTGGCTAACAATGAGAAATCCTGCCTATCTTCTAAATTTGATGTATTCATGAGCCTAACAATGATTGAGTGCTATAACTCACTTTTTCTGATTATTTTGTTTAGAAATTTTAGAGCTTGAACAGCTAGAAGTTAGCCCAAGAAAAATTATTCCTAAAAATAACTGTATCTCCAAGTTTCAACAGTAAACATCTTTAAAAAAATAATAAATAACGATTTTTTTTCTGGTCACTCTTGTATAGACTTAGCTGATATAAACTACTTTCATGCTACCTTAAATGAGACATTTTGACAATGTTGTTAGAATTCTGATACAGAAGCCAAAATTCTGCTAGAATTTATGCTTGGGAAACAATTGAGGTATTTAATCCAAACTGCATACAATTCAGCTTTAACATCCTTTAAAAAGTGCTTGTAATCCTGGAAACATCATGTATCTTTGTTATTTCTCCAGCTCCTTTTAATCTCGAGAGCAAGGATCCCTTAACATTAAACCTGGACAGTATGGATCAGCAGATACCACTACAACATTGTCCCCTCTAGGCTCTCAAACATTTCCCAAATGGAGTCAAGTGGTAAAAAAGACACTATCATAATTCCCTTCTTCTAATGTTCTTAATCTTTGGCCACAAAACCTTTGTATTGAATGCCTGATACCACTTATGAAAATGACGGCGATGCCTGCAAGTTTCTCACACCTATATATTTTTCCAGACTTCTCCCTACTTCATATTATTTTTACTTTTCCGAGTTTCATTTATGACATATCTTTTTTTTCCTAATAAATTTCTTAATTGCTGGTATATTTGCCATAGGATATAGGTGATACTAAACCCTTTGTTTTGTTTTAAAATAAGGAACTTGGTCAGCAAAGTAGACTCTATCATTTGGGTTTTTCCTTAGTGAAATAGCTGAAATGAAGGTCAAATTGTTCAGAGATTCATTTCAGGCATCATTACGTTAAGTAAGCATCACTGTGTTAATCTGAAAAATTATTGGTTTGCCTCTTCTGTGGCTCCCTTCCAACAGCTATTTTCCAGCACTATTGTATTGCAATAGCAGGGACACTACTGCAATGCAGACTAAGAGTGTATTTTAGTGTTGCTATTCATCTTGAATATCAGCTTTCAAAGACATCCAGAGAGCTCTCTCATTACGGGCTGTGCTGCCTGAATCATGTGACTCTGAGAAATAAATGGGGGAAAGATGTCGTTCCAATACCCAATCCTAAATTCATTGTTTAGCTAACAATATCTGTGTTGTCAGTCTCTACAATCATAACAAAAAGACTTATGTTTTGATGATTTTGAAGTAATTGTCTATAAAAACAATAAATAATTCCCTCTTAGTTTTTTACTCTGAGTTTACTTGTTATAGTTAAGCCAGAAGTTTATTGAGGAATTTTAGGGGAGGCATTTGTAGAATAAGGCTTAGCTACTCCCTGTTGACTTTAGTAGATCCAGAGAACTGACAGATCCCTTAATTTTGGTTCCACAG
Seq C2 exon
AATCATCCTGATGTTGCAAGCAAATTGGCTACTTGTCCCTTCAATGCTCGCCACCAGGTTCCTCGAGCTGAAATTAGTCATCATATCTCAAGCTGTGATGACAGAAGTTGTATTGAGCAAGATGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170627-GTSF1:NM_144594:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF052537=zf-U11-48K=WD(100=79.4)
A:
NA
C2:
PF052537=zf-U11-48K=WD(100=62.8)
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:
GACTCCCTGGACCCTGAGAAG
R:
ACATCTTGCTCAATACAACTTCTGT
Band lengths:
224-1993
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
- Pre-implantation embryo development
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)