HsaINT0132632 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153515784-153519212:-
Coord C1 exon
chr2:153519117-153519212
Coord A exon
chr2:153515871-153519116
Coord C2 exon
chr2:153515784-153515870
Length
3246 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATT
5' ss Score
8.88
3' ss Seq
TTTTTTTTTTGTCCCCGTAGCAT
3' ss Score
11.19
Exon sequences
Seq C1 exon
ATCCGTGAGAGATTTGTAAAAGAGCCAGCATTTGAGGACATAACTCTAGAATCTGAAAGAAAACGAATATTTAAAGATTTTATGCATGTGCTTGAG
Seq A exon
GTAATTTTAGAATTCTCATATACAAAATATATAAAATATAAACAAATTGAAGAACTTAGAATGATGAAAGTATGTTGCTTAATATTCACTGCTTTTATACAAATGTACTTACCTGGATGGTTAGAGAATGGTTTTTTTCCTATAAAAACTGCTTTTAAGTAAAAGAAACTATTAAGTTTCCATGGGAATATAAAGATTTGTATGTGAAGACTGTTTTGTATTTTTAGAAAGTTTTAGAAATTGAGCAGTTTGGCAGCCACATGGATTGATTGACTAATAAAGAAAACTTGAAATTTTTCTTGTAAAGCAGATAGAAGACAGCTTTTAGGCACATTTGAGGTATTATACCACATTAGCTGTGTAGAAAAGAAAGTTTCTGGAAAGTAATGGAATAAATGGTAAGTTTTTGTTAAAATAAGCAATGAAACAATAACATCTCAGGTCACTTTAATAGGTAAGGTTCACTGGGCACGGTGGCTCACGCCTGTAAAACAAGCACTTTGGGAGGCCAAGGTGTGTGCTGATCACCTGAGGTCAGGAGTTTGAAACCAGCCTGGCCAACATGGCGAAATCCTGTCTCTACTAAAAATACAAAAAAATTATCAGGGAGTGGTGGCGGGCACCTGTAATCCCAGCCACTCAGGAGGCTGAGGCAAGAGAATTGCTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGATCATGCCACTGCACTCCAGCCTGGGCAACAGAGCGGGACTCCTTCCCCAAAAAAAAAAAAAAAAAAAAAGTATTTTGATGACAGTTTCAGTTAGGCCCTTGTAAGTATGCTGAATTGACCAATAATTATTGAATAATAGTATTCGATGCCTATGTGGGCCAGTGTTCTAATTGCTTTATGTATATTATATTTATGAACTGAATCCTTTCAATAAGCCTGTGAAGTTAATAGGTGAACAAACTAAGGCAGAGAGAAGTAAAGTGACTTACAGGGTTGGAAGCCGGGCATGTTGACCTTGGTCAGTGCTTTTAACAAGTATGCCATGCTGTCAGTTTTAGAGTAGCTAATACTTTATAAGCTAAAAACTAGTAGGTGCTTAATATTACAGTGTTGCATTGTAAATGGGCATAGGTCACTAAATTGACTATTTCCTATTTCTTGATTTATTGTTCTTGATTAATATAATGTTAACCACAGTTTTTTCTGTACCATGTACTCACGAAGGCCCTGTATTGTTTCACAGCTGCCTCTAGATGTGGTCCTGTTGGCCTTTTTTTTTTTTTTTTTAAAGCGGGGTCTCTGTCATCCATCCACTCCTAGGCCAGAGTGCAGCGGTGCAGTTATGGGTCACTGCAACCTTGAACTGTTGGATTCAAACAATCCTCCTAAGTAGCTGGAACTGCAGGCACGTGCCATCACACTTGGCTTTTTGTGGGGCTTTTTTGGTTTTTGTTTTTATAAAGATGGGATCTTGCTGTGTTGGGCAAGCTGACCTCAAGCAAGTCTCCTGCCTTGGCCTCCTGAAGTACTGTGATTATAGGTGTGAGCAACCATGCTGGGCCTCTAGATCTTTTCTGTGCCAAATGTAGTGCATACCAGAAGCATCTGCATTACCTAGGAGCTTCTTAGGAATGCAGAACCTTAGGCCCCATGGGGCAGAAATCCTGCGTCTGACTTCATTTTAACCAGATTCCCAAGCATTAAAATATACATTTAATTTTGAGAAGCTCTGCTCTAGATAGTGACTAACCTATTTTCCCCCAGTTCAAGAGTCTACAGATTCTTTCATGATCTATACTGGGGGTAAAGTAGTTAGGTGGTAAATGGAGTAAAAATGGTACCATAGGGAAGGGCTGAACACATTCAGATTTTGGGGCCTTAATAATCTGAGGCTTGAGGTATTAAAGAAAGGTAGGTTAGCATTCAGTGAGATCAAAAGGAGAATAGTCCATTCTGAGATCCAGATTTTCCATTTCCACTTCTGTAACTGAGGTAGAATTTATTCTCAAAGCCATAGAAATGTTTAGGGGCAAGGAGCTTGTACTGTAGCACCCCCCATCACTGCTAACCTAGTAATTGTTTTAATAAGTAGAAATCCACAAAGACAGCATATGGATGTCTAACAATGTCTTGTTTGAGGAGGAAGGAAATGGCTCCTTGGGGGAAATGAAAGAGGGGTAGCAGATTTTGCATTTATTCTGACATCAGCCTTATATATCTCAATTCAAGGATGGCTCTCAGGTTGTTCTTTATCTTAGTGCTTGGCCTAACTTGCTGACCAAAGCCAGATTGATTACAAAAACCATGTCTGAGTGTCATTGTATTTGACTGTCATTAAAAGCAGATGTCACTGCATATTACACTTTTCTTCTAAATCACACCATTCTCTTCCTTAAAAAATACTTTTTCAGGCTGGGCACAGTGGCTCACGCCTGTAATCCCAGCATTTGGGAGGCCGAGGTGGGCGGATCACAAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCATGGTGGCAGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCTTAGATCACGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAACAAACAAACAAAAACTTTTTCAGCTGGGTGCAGTGGCTCATGGCTGTAATCCCAGCACTTTGAGAGGCCAAGGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGGCTGGCCAACACGGTGAAACCCTGCCTCTACCAAAAATGCAAAAATTAGCTGGGCGTGGTGGTGTGCACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAAGCGGAGGTTGCATTGAGCCAAAATCGCACCACTGCACTCCAACCAGGGTGACAGAGCGAGACTTCGTCTCAAAAAAAAACAAAAACAAAAAAAGCCCTACTTTTTCTACTAACAGTTTTTAACATTGTTTTGTTTAGATGTCTAAATGAGTGGGTATAGGATGGGCAAGAAGGAAAAGAAAAAAAAATTGACAATTCTTCACAGTTTCAAGGGATTACATTTCTATATATTGTAGAGTTTTACTCTAAGAACTTACTTCCGTAGCTTTTTAAAGATTCTTTACAGTCTGTCTACAGTAAGTGTAAATTCTTGAAATTTTTTTTTTGTCCCCGTAG
Seq C2 exon
CATGAATGTCAGCATCATCATTCAAAGAACAAGAAACATTCTAAGAAATCTAAAAAACATCATAGGAAACGTTCCCGCTCTCGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.188 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(50.0=81.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
SPECIAL DATASETS
- 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)