HsaINT1028863 @ hg38
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr12:47757866-47758645:-
Coord C1 exon
chr12:47758551-47758645
Coord A exon
chr12:47758079-47758550
Coord C2 exon
chr12:47757866-47758078
Length
472 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CTTTCCTCCCCGTGTCACAGGTG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GGATCCCCTTATCAAAGCTGATGGGGGTCGCTGGGGACCCCCCAGCCTTTTGCTAGAGCCTGCACGGCTGTGCGAGCTTGAAAAGAAACATGAAG
Seq A exon
GTGGGTAAGGTGGGGTCAGGGTTGAGGAGGAGCAGGAGAGGGCGGGAGAGGAAGCTGACACGGTGGGGAGTTTGGGTGGGAGAGGGAGGGTTAGTCAGGGCTGAGGAGGAGAGGAGAAGGGTTTAAGCCGAAGCTGCATTTCTGGGAGACCTAGTGAATCTATAGCTTCATACTGGGAGGTAGTGGAGATCCCTGCAGGGGCATGGGCAGTGAGATGGGACAGAATTCCAAAGAGGACTAAGAAGGGCCTGATCTTTTCCAAGAGCCAGCTGGAGACCCCTAAGTGCGCCAGACCGGCAGGCCCCAGTGAAGGTCTTCCTGTTCCTCCCCCCAGCTCCTGGCAGGGTTGCAGCACCTCCGCCTGACCAGTCCAGAGGACTCTAAGGAAGTAGTTCTGCCTGGGGCAGTTGTACTGTGGCCCAGCCGCCCCAGTCGTGTCCCATGGCTGTCCACTTTCCTCCCCGTGTCACAG
Seq C2 exon
GTGGGCTGGCCAGGTGAGAGCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCTCTGGGAGCACCGCGGGTGGGAGCCCTCCCTGACGTGGTGCCGGAGGGGACACTACTCAACATGGTGTTGAGAAGGATGCACCGGCCCCGAAGCTGCTCCTACCAGCTGCTGCTGGAGCACCAGCGTCCGAGCTGCATCCAGGGGCTGCGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337:ENST00000449771:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.022
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCCCCTTATCAAAGCTGATGG
R:
CAGCCCCTGGATGCAGCT
Band lengths:
302-774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains