HsaINT0132644 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50024327-50025327:+
Coord C1 exon
chr12:50024327-50024408
Coord A exon
chr12:50024409-50025183
Coord C2 exon
chr12:50025184-50025327
Length
775 bp
Sequences
Splice sites
5' ss Seq
TTCGTAAGT
5' ss Score
9.77
3' ss Seq
CTTCCTTTACTCATTTCCAGATG
3' ss Score
10.62
Exon sequences
Seq C1 exon
GTCGGTTCCCGATTCTGGTCCCCGGCCCCCAGCAGCGCCTGCCCCCTTCCCACCGGGGCCCCCCATGATGCCACCACCCTTC
Seq A exon
GTAAGTTTTATGTCTTTCCCTGGGCTTGGCTTTTCCAGCCTGCACCCCCAACTCCCCAGCCCCTAGCCACTGCTGCATCACCAGCACAGTTTTCCTGTAATGCCCCTTTTGCTGACCTTGGAAGAGGGATGGTTTTACTTGAGCATTGGGTTGGGGAGAGCTGTTGTGAAGCCCTCAGTACATAACATTGACAATTCCCCCTTTGTCTTTTTGACCTTAGGACACACTGGGGCTAGAGGTAGGAGAAGTGGAAGGGAAAAGACCCCATTAATGTGAGGGCAGGGTGGGACTATCTATCTCTTTCACTACTCCTTACCTATGCTCTTTAAATATGCCACAGAATTCGGGCTGGAATGGCATTGGTGGTCATGAGTTGGAGAGAAAGGGATGGGAGGCAGGGGACTGGGGTACTTGGGTACCTGGATACCTGCCTTCTGCCCCTTCATCTGAGAGGCCTCTTTGGGGGAGAATTGCTGAAGAGGTGGAGCCTTCCAGTCTCAGTCTGGTGCTGTTAAACCTCCCTTATTCCTTTCCTTTCCCGTTACAATTAAGAAGCTGTGTGCTTGCCTGTTAGACCCCAGTTGTCAGTCTTTCTCAGTGGTGAGGAGGGAGGCAGTTTCATGCCTTGTGCTTCTCAAACTAAAGCCTTGGAATTGCCTCAGAGCAGGGTGGAGGGTTGGGGAGGGAGGTGGTGGATATTTCCTGACAGGTCCTCTCTACCTCTGACAAGGCGATGTCTTCCCTGCTCAGTATCTCTTCCTTTACTCATTTCCAG
Seq C2 exon
ATGCCCCCTCCAGGGATCCCCCCACCCTTTCCTCCGATGGGGCTACCCCCCATGAGTCAGAGACCACCAGCTATCCCCCCCATGCCACCTGGCATCCTGCCCCCAATGCTTCCACCAATGGGGGCGCCACCACCACTCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.991
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCCCGATTCTGGTCCCC
R:
CTGTGTGAGTGGTGGTGGC
Band lengths:
223-998
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)