HsaINT0137420 @ hg19
Intron Retention
Gene
ENSG00000136237 | RAPGEF5
Description
Rap guanine nucleotide exchange factor (GEF) 5 [Source:HGNC Symbol;Acc:16862]
Coordinates
chr7:22200136-22202159:-
Coord C1 exon
chr7:22202015-22202159
Coord A exon
chr7:22200234-22202014
Coord C2 exon
chr7:22200136-22200233
Length
1781 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
CATTTGTCTTTTTTCTCCAGACC
3' ss Score
9.93
Exon sequences
Seq C1 exon
CTATTCTGCTAAGAAGTATCAAGGCAAAGAGGAAAACTCAGACGTTCCGCGTAGGAAACGTAAAGTCTTGCATCTTGTTTCCCAGTGGATTGCTCTGTACAAAGACTGGTTACCTGAAGATGAACATTCAAAAATGTTTTTAAAG
Seq A exon
GTAATCAAACATTTCCAGATATTCTTTGATGCCAAATAACTGATTCTATTTTTAGTTATGCATTTTAAAAATCTCATTTGTAGGTAACAGTCATTCAGCTTTCTTGTGATAGTCAAGTTGTGATTCAGAGAATATTTAAGTTTATTTTGACTTCTGAAGCTTGATATTCTCTATCTAAAAAGTCATGGAAATTTTGATTGCTAATGAAATAATTAAGGAAGGTAAATCAAAACATTCAAAATTTGATATAGCTTAATATGTTGATATTCATTATAAGTTTAAAGTAACCAGTCCTCTATATGTAATATTTGCATAAAACATTATTTATCATTTAAAAACTATATTGACAATGTATGTTCTTTGAAACATTTGTCAGACATGGTATACTTTGAGAATTTTAAGCAATAATTTGTAAAATAGATATAATCTAGTTTTACATTTAGAGTGAGACAAACTGATTTATTTTTTCTAATTAATAGGCTTCAATATCTTTTCAACACAGATGATTATCTGGAGAGATGATTAGTAAGACAGTTGGATTCCTTTGGCCACCAAAATCATATTAAGTCTGCAGGTTAGGACAGAGAAGGAATACAATGGAATTCTAGCAAGGAAGAGTTCTAGTTCAGAGTAGGCAACTGCCTAAATAGACTCAGCCTTTCATGAAGGAAACTACTTTGAATTCAACATTCAGTTGTCATTTAGGCATCCAGTTAAAAACGAGTCTAACCAACTCTTTAAACTCATGTTGTTTGCAAAGCAACTGCTTAATTTAATTCAATTGACTTTTTTCTCCCAAATGATTATGTGGAATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGAGACAGGGTCTTGCTCTGCTACCCAGGCTGCAGTGCAGTGACGCAGTCATAGTTCACTGCAACCTCAAACTCTTGAGCTTGAGAGATCCTTGCACTTCACCCTCCTGACTATCTGGGACTAAAGGCATGCACTACCACACTCAGCTAATTTTTTCTTTTTAGTAGAGATAGAGTCTTGCTTTGTTGCCCAGGCTGGTCTCGTACTCAGCTCAAGCAGTTCTCCCTACTCAGCCTCCCAAAGTGTTGGGATTTACAGCCTGAGCCACCACACCCAACCTATATTATTACTATTATTTATTTATTTGTTTACTTATTTATTTATTTTTTGAGACGGAGTCTCGCTCTGTCGCCTAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGGATTACAGGCGCCCGCTACCACGCATGGCTAATTTTTTTTTTTTTTTTTTGTATTTTTAGTAGACACGGGGTTTCACTGTGTTAGGCATGATGGTCTCGATCTCCTGAACTCATGATCTGCCTGCCTCAGCCTCCCAAAGTGTTGGAATTACAGGCGTGAGCCACCATGCCCGGCCTATTATTTTTTAAGATATAGAATGGGCTGGAAATCTCTAGTAGCCAGCCAGCTAGGGATCTCTAGAATTCTCTTTCCAGAATTTCCACCTATGGCCCTGAAAGCAGATAGAGAGCCATGGCAGTTGAGAGAGGAGCTGCGAGTTATGATCCCATTCTGGATCTCATTGGCACCTGGTGAAACCCGTACATTGTCCTGAATCCCTCCTTATTTCCTGTGTTAGGATAGCCATGGTATGAGTCTTAATCCCTACAAAATGGGCATTCAACCACTGAGCTCTCATTTGTCTTTTTTCTCCAG
Seq C2 exon
ACCATATATAGGAATGTACTGGATGATGTTTATGAATATCCAATACTTGAAAAAGAATTGAAAGAATTTCAAAAGATACTTGGAATGCACCGTCGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136237-RAPGEF5:NM_012294:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(43.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(12.7=27.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCTAAGAAGTATCAAGGCAA
R:
GACGACGGTGCATTCCAAGTA
Band lengths:
238-2019
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)