HsaINT0119633 @ hg19
Intron Retention
Gene
ENSG00000006712 | PAF1
Description
Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25459]
Coordinates
chr19:39876270-39877212:-
Coord C1 exon
chr19:39877122-39877212
Coord A exon
chr19:39877044-39877121
Coord C2 exon
chr19:39876270-39877043
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
CTCTCTCCACTCCCTTCCAGATG
3' ss Score
10.85
Exon sequences
Seq C1 exon
GAGGCACGGAAGGCCCAGCTAGAAAACCACGAACCGGAGGAGGAAGAGGAAGAGGAGATGGAGACAGAAGAGAAAGAAGCTGGGGGCTCAG
Seq A exon
GTAAATCTGGACAGGCCAGACTCTGGGAGCCCTGGGAGGGTGGAAAAGTGGGTTTCATCTCTCTCCACTCCCTTCCAG
Seq C2 exon
ATGAGGAGCAGGAGAAGGGCAGCAGCAGTGAGAAGGAGGGCAGTGAAGATGAGCACTCGGGCAGCGAGAGTGAACGGGAGGAAGGTGACAGGGACGAGGCCAGTGACAAGAGTGGCAGTGGTGAGGACGAGAGCAGCGAGGATGAGGCCCGGGCTGCCCGTGACAAAGAGGAGATCTTTGGCAGTGATGCTGATTCTGAGGACGATGCCGACTCTGATGATGAGGACAGAGGACAGGCCCAAGGTGGCAGTGACAATGATTCAGACAGCGGCAGCAATGGGGGTGGCCAGCGGAGCCGGAGCCACAGCCGCAGCGCCAGTCCCTTCCCCAGTGGCAGCGAGCACTCGGCCCAGGAGGATGGCAGTGAAGCTGCAGCTTCTGATTCCAGTGAAGCTGATAGTGACAGTGACTGAGTCCCAGGGCATTCAGGGCTGGTTCAGACACCATTATTGTGAGCAGCAAAGCACTTTTCTAGTGGTCTGTTTGTGAGCCTTTCACTTGTTTGTTCCCCACCCCCAAACCTTTGCTGTTAATAAAGTCAACTTCTCTTTACTTCCCCTCCCAGCCCCTATGATGTCATTCAGCCCAGCACATACCTCCCGCAACCCCCAGGTGCTCAAGGATCTTGGCTTGAGGCTTAGAAACACAGGCCAGAGGCAGGGCCAATGGTTTCCCACAAAATGTAGCACAACGAAGGTCAGAATTCGTTTTTTTTGTTTGTTTTTTTTTTTTCCAAAATAAGCCCAGACCATTAAACAAGTGAAACTCCAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000006712-PAF1:NM_019088:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.935 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF039858=Paf1=PD(15.8=93.5)
A:
NA
C2:
PF039858=Paf1=PD(12.1=37.0)
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:
CGGAGGAGGAAGAGGAAGAGG
R:
CTCACCACTGCCACTCTTGTC
Band lengths:
182-260
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)