HsaINT0119639 @ hg19
Intron Retention
Gene
ENSG00000006712 | PAF1
Description
Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25459]
Coordinates
chr19:39879587-39879838:-
Coord C1 exon
chr19:39879733-39879838
Coord A exon
chr19:39879656-39879732
Coord C2 exon
chr19:39879587-39879655
Length
77 bp
Sequences
Splice sites
5' ss Seq
TCAGTAATT
5' ss Score
0.5
3' ss Seq
CCTTGTTTTTGTTCCACCAGATC
3' ss Score
10.3
Exon sequences
Seq C1 exon
GATTGGGGTTTCTGTGAAGCAGCAGTTTACCGAGGAAGAAATATACAAAGACAGGGATAGCCAGATCACAGCCATTGAGAAGACTTTTGAGGATGCCCAGAAATCA
Seq A exon
GTAATTGAGGGACTGGGATGGGGAGAGGCAAGGGTGCGGCTGCAGAGCTCCTCCTCACCTTGTTTTTGTTCCACCAG
Seq C2 exon
ATCTCACAGCATTACAGCAAACCCCGAGTCACACCGGTGGAGGTCATGCCTGTCTTCCCAGACTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000006712-PAF1:NM_019088:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.213 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(21.3=100),PF039858=Paf1=PU(0.5=2.8)
A:
NA
C2:
PF039858=Paf1=FE(5.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGGGTTTCTGTGAAGCAGC
R:
AGTCTGGGAAGACAGGCATGA
Band lengths:
168-245
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)