HsaINT0132621 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153529492-153530220:-
Coord C1 exon
chr2:153530112-153530220
Coord A exon
chr2:153529557-153530111
Coord C2 exon
chr2:153529492-153529556
Length
555 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTA
5' ss Score
7.04
3' ss Seq
TTCATTTAAATTATTTTCAGCGG
3' ss Score
6.66
Exon sequences
Seq C1 exon
TTTTACTCCCAAAAAAGAAGAGGAGGAGAGCCAACCAGCAAAGAAAACATACACTTGGAATACAAAGGAAGAGGCAAAGCAAGCTTTTAAAGAATTATTGAAAGAAAAG
Seq A exon
GTATTAATATTGCAGATTTTTATTGTTTCTTAGCTTTTTGACATCAAGCATGTATTATGGATTTTTATGTGATGTGTAATAATTACCCAACAAATGACGTTACTCTTTAATTAAACCTTGATGGTATTGATAATACCAATCTCATGAACTGTTGTAACTGAAAAGCAACTAAATATGTCTTTTTTTTTTTTTTTGAAGTACACTTTTGTGAAACTTTCAACACAAAAACTATTGTGTACAAGGTACTACACAAGCACATTTCTACCCAATATTTAATGTAAGGGTTTTTTTTTAATTCATAATAGTTATCTTTTATCCATAGTCTAAGAAAAAAGCATTTATGTTCTATTTAAATTTCAGTTAAAGTTTTCATTTTAGTTCATAGGTGTATTACACAGATTTGCCTTCAGTAAAAAACTATTTTTTATAACTTGTTTCAAACTCCTGCAAAGGGAAATGCTTGATGTTTGCAGTTAGTATTATACTCAGTTTCCTATTATGTGACTTAAACTATTCTTGTGTGAAATTTTAATTTTTCATTTAAATTATTTTCAG
Seq C2 exon
CGGGTACCATCGAATGCTTCATGGGAGCAGGCTATGAAAATGATTATTAATGATCCACGATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.730 A=NA C2=0.227
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(24.0=32.4)
A:
NA
C2:
PF0184614=FF=FE(42.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]
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)