HsaINT1028864 @ hg38
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr12:47748454-47748931:-
Coord C1 exon
chr12:47748819-47748931
Coord A exon
chr12:47748543-47748818
Coord C2 exon
chr12:47748454-47748542
Length
276 bp
Sequences
Splice sites
5' ss Seq
CCGGTAATA
5' ss Score
5.56
3' ss Seq
AGATTGGCCATTTCTGCTAGGTA
3' ss Score
4.56
Exon sequences
Seq C1 exon
GATGTGGAGGCAAAGACCATGCGGCTGGAAGAACATGGCAAAGTGGTGCTGGTGCTGGAGAGAGCCTCTCAGGGCGCCGGCCCTTCCCGACCCCCAACCCCAGGCAGGAACCG
Seq A exon
GTAATACACCTGCCATGCTCCCTCTCCACACTGTCCCTCCTTTCATTTCCCAATCTTTGCTCCCTTCCCCTGTGTCATATCCCTGCCCTCTGGCCACTTGTGGATGGAGAGGTATTGAGGGACCAGGATGTGCCTGCTGAGCCAGTCTCCTCCCTGCCCTAAGGTGGGACAGGGCTGGCTAATGGAGAAAAATGATGTAATTGATTATTGATGTCTGCCCAGGTGTGGGAGTGGGGAGTAGTGGCACCAGTGCCAAAGATTGGCCATTTCTGCTAG
Seq C2 exon
GTATACAGTGATGTCTGGCACCCCAGAGAAGATCCTAGAGCTTCTGTTGGAGGCCATGGGACCAGATTCCAGTGCTCATGACCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337:ENST00000449771:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.474 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.4=5.3)
A:
NA
C2:
PF0061815=RasGEF_N=PU(25.5=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTGGAGGCAAAGACCATGC
R:
CTGTTGGGTCATGAGCACTGG
Band lengths:
201-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains