HsaINT0132624 @ hg38
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:152670231-152671381:-
Coord C1 exon
chr2:152671273-152671381
Coord A exon
chr2:152670382-152671272
Coord C2 exon
chr2:152670231-152670381
Length
891 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTC
5' ss Score
6.8
3' ss Seq
TATTCATACTTTTGCTATAGGAA
3' ss Score
8.3
Exon sequences
Seq C1 exon
AAAAGCAGAGCAAATGTTTGGAGAGATGGAAGTTTGGAATGCAATATCAGAACGTGATCGTCTTGAAATCTATGAAGATGTTTTGTTCTTTCTTTCAAAAAAAGAAAAG
Seq A exon
GTATTCTTTATTCTTAGTTATTGGTATTTATAGATAACACAAGATGTTTCCTCATTCGGATGAGGATTGGTTTTATAATATGTACATTTTTCTGGCTTAGTTTATCCAGTTTATGTGGTATAGCAGATTTATTTATTGGAAGTAAAATTTAATGATGGAATGTATAGCTTCTGTAATAATCTTCTTTATCGTTCATGTAGCATATTAAGTACTGATGTAGACTCAGTGGGTACTCATTCAATTATTTGTATTGTCATTAGTTGGCTATCTTATGCTCACTTTGAAAAGATACCTTTTTTGCTCATTAGGTTTAAAAATGCTGGGTTTTTTTGCTTATAACCAGCATGATTGTTACAAGAATGACAGCAACATGCAGTTGTTTCTACTAAACTTACAACATTTTAAAATACCTATTTTACTCATGTCTCTTTTTCATTGTGCACTATTATATTTTATGTTATCTGGTTTCCAAGGAACACATACAGATGCAAGTATTATCAAATTTAAACATAGCTGAAGGTCATTGAAGATTTTAGCATTTACCTGCAATGCGACTTGTCCATAGTAACCTTAGTTTCAGACTGTCTGTAATACATAGTGGTAGAAAGGTTTATGTCGTATGGGGGAAAAGCCAAAAACATGGTTTCCAGATTCTGGCTTTTAGAAGGAGGTGGAAAATTTGAAGCTAAGTACCAAAGCCAAGCGCTTAGGAAAGAGCATTAGCAAAGTCAGCAGTGTGGCCATTTAAAGTAAATGAAATTTACTTGAAGTTTGACTTAACCTTTGCAATTTGGTCATCCGTTAGAATATAAAGAAGCCGTCACTAATTGCAATTTAAATATCTTAATTTCTTGGAACTTTGAAACATACATATTCATACTTTTGCTATAG
Seq C2 exon
GAACAAGCAAAGCAGTTGCGAAAGAGAAATTGGGAAGCCTTAAAAAACATACTTGACAACATGGCTAATGTAACATACTCTACCACTTGGTCTGAAGCCCAGCAGTATCTGATGGATAATCCAACTTTTGCAGAAGATGAGGAGTTACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504:ENST00000410080:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(54.0=73.0)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
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:
AGCAGAGCAAATGTTTGGAGAGA
R:
TGTAACTCCTCATCTTCTGCAA
Band lengths:
255-1146
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