Special

HsaINT0137376 @ hg19

Intron Retention

Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48128453-48131876:-
Coord C1 exon
chr12:48131805-48131876
Coord A exon
chr12:48131469-48131804
Coord C2 exon
chr12:48128453-48131468
Length
336 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
TGACTACTCTCCTCCACCAGGCT
3' ss Score
8.24
Exon sequences
Seq C1 exon
TGCCTCTCTCACCACTCAGAAGCCGAGTTTCCCACCTCCACGAGGACAGCCAGGTGGCGAGGATTTCCACAT
Seq A exon
GTAAGTGGTGGGCGATGGTGGGTGGGCAGGGAGGGGGTGCTTATGGTAGTTACCCATGGCTGGCACATCCTAGGCACTTGCCATGTGCCAGGCACGGAGCCCGGCCCTTCCATACATGATGTTGATAATGTTCAGCCTCTGTGCTCTGAGCCAGGGGGCTCTTCGGTCCCCTCACCCGTGGGGTGGGCAGGGACAGCCGTCTTTAGGAATTGGTGATGGGAAGTGGTTGGTGGGTGGTGGAGGGCAAGAAGGCAGATGTGATATGGCTCCTTGGAGGGGAAAGGTTGGGTTCCACAAAGGGGCATCAGTGCCTCCCTGACTACTCTCCTCCACCAG
Seq C2 exon
GCTCGGAGCAGTCCCTGAGCACCCGGAGTCCAGCCAGCACCTGGGCTTATGTCCAGCAGCTGAAGGTCATTGACAACCAGCGGGAACTCTCCCGCCTCTCCCGAGAGCTGGAGCCATGAGGAGGGGCTGGGACTGGAGCTGGAGCAGGCACTTGCAGCCGGGAAAGCCAGGGTGTGCCGGGCCAAGATACTCACAGGCTGGCCACAGCTGGGCAAGGCTCTCCGTGGAGTGGACTCGAGTCCCTGGAGCAGGCAGTGTGGAGGCAGCCATCCCCTGTGATGACTGGCAGCTAAGGAGGACCTCGGAGTGGACCCGAGCCAGGAATAACGAATGACCCAAGGCCAAGGAAGGGAGGACAGAGAGGCCCCAGGAGTGGGTGGAGAGTGGAGTGCGCTGGGACGTTGTGTGCAATAGAGAGGTCTCCACACCAGATGTCTTCCAGATTCTGTGCCTCTGGCTTTGTTGTCCAGCCAGGCCTGCAGTTTATTTTCACAGTGGACAGAGAGAGAGAGAGAGGCTGCATGTGTGTACCGTGTGTGGCAAGGGCAGGGCCTTGGCCTGGGGCAGGGGCCCCCTGCTTTCTTTCCACAGCTTTCTTCCAACAGCAGGCAGTGGGGCTGCGGGCCTGTGCGGTGGTCCCTGAGGAGCTTTATTGTTACTGTCAACATAGTAGTATGTTCCAGGCCAGCCCAGAGTGGGCGTGGCAGGGAGGCTGAGGCCCCGCCCTCTGGGAAGGAGCTGTGGAGGAGAAGCAGCCCCATGCTGGGCACGGGCCAGACTGGGTCCAAGATCCTGATGCCACCCAGATGTGCCTCCAGGGCTCTGGCCAAAGGGCGGGCTGGAGCCTGGAGCCCCTGTCAGCAGCCAGCCAGGGTGACCATCAGCTCCCCGTGGTGGTCCAATAGGACTTTACAGTCCAGATGCAACTGACAGCTTCTTCCCAACTGCAATCCCCGCTTTTCCACACTTGAGCTCGTCCTGGCCTGTTGGGCCAGGCTTCTGGGGTCTTCTGGGGGTGGCTTGTGATAGAAACAATGCTGAAGCTTCCGCGGAGAGCCCGTCGCTTGTTGAGGCCCAACAGACTTCCAGGAAATCAGGGTTTATCATCAGTGTTGAGAATGGTCCCAGCAAGCTCTGGTCATACGAAGTCCTCTCTTCCCTGCCCCTTCAGCACTTCCCCTAGGAACCAGCTACTGCCAGGACGCCTCTTGCGAGGCAGAGCTCACCCAGGAAGCTCCAGGGACTCCACCCTCTTGCCTTGCTATTGCCCTGAGTCCTGGCAGCAGGAGGCACTTGTCTGGCCAGAGAGAGAACTCATGGCCCCTGGCATGACTCCTGAGTAGGTATTGAGGCTGCAGGGCCTTGGGCGTCCAGAGGCAGCTGGTATGGCCCCTCTGCACTTCAGCCCCATGGATGTGGATACACAGGCCTGCTGCTTCCAGAAAGGGTCAGAGCCTTTAGCAGGGAGGCAGCACAGCTGGGCTTAGACCTCAGGTCACTAAGTGAATCTGAGCAAGTCAGTGAACAGTTCTCTTCCTTCATTTCTCCACCTGTAAGCCAGGTATGATAAACGCCATACAGCGCTTAGTGACAAACACATAAAACTGTAGCTCCTGCCTCTGTAGCAGAGGTGACAGCCAAGGGCAGTCCTGTGCTATCCAGGCCTGGTAGGGGGGCAGCCTCGCCTCAGTTGAGGGCTGAGGGAGAGACTGAGGTGCAGCAGATGGCAGTGGTAACCAAACCAGTTCCCTTGCCGTGGGTGGGGACACAGGAGAAGCACGGAAGCATCTGGAACTGAGCAATCAGGACAGGAGGCTCAAGCCTGGGTGAGTCAGGAGTCCGGGGGCTTTCTTTTCATCCAACCCATTGTCTGCTGGTGTCTCGGCAAAAGCCAGCCAGCCAGCCGTGGCCCTTCACCGTTCTTCAGACTCTAGGGTGAGCCCAGCCCAGCGACACAACAGAAACCAAGTGCCACGGGGGCCGGTGTCCTCCACCAGCATTTCTCCTCTGGTCACATCTACGTCCTGATGGGACTTCTCCCTCCTCCTTGGACCATCAGCTTTACAGTCCAGACCACCCTGCAGCCACCCGGTGGTCTCCCAGCTGCCCCAGTCTCGGGCAGGATGGCTTTTGAGCCTGTTGGGAGAGACCTTGCCAGGAGAATGGTGCCCAGGGCAGGCAAGAGGACACAGACTCTGGGAGCTAGAAGAGTTGCGGCCCAGGGGGCCAGGCCACTCCCAGAGGACAGGAGGCCCAAAAGCGGGGAAAGGCTCCATGTTACGGTGGCCCCATGCTGGGAGTTTGTGCTGCCTTCTGTCTCCCTGACTGCCCAAGCGTGGGGTGGTGTGGGGCAGGAGGCATCCTCTGGTGTTCCCTAGCAGCCCAGGCTGTGTGCAGGGGCTCCCATTTTGTGTCTCAGCTGCAAGAAGGCCACAAAGGGAGGAGGGGCTCATGGGACTGCTGAGAAGAAGGTGTGCAGAAAGGGAGTGTGGCCCTAGATCAGTCCTTTAAAAAGCCTCTGTTACCTGAAAGGAGGTCAAGCAGAGAGGAATGGCTGCGTGTGTGTCCTACCGGGCAGGACAGGACAGAGGGAGGTCATTGTTACACACACATCCCCCCTCCTTTCCTCCTTCCCCTCCACTTCCCTGTGAAGGCCTGAGGCAGGCTGTGGCCAGGCTCAGGCCCTGACTGTGGGGTACACACCAGGGAGGGCCACGCCTCCCCACAGACGGGGTGGAGTGGTCAGTGGAGCCAGCACCCTCTGCTGCTTCAGCATCTCCGCCTGGAGCCAGCTGTCCCCTCTCTCTCAGGCTCCATCCGAACAAAAGGAAGGCAGAGCCTGAGATCCGGCACCCCATCCCCCTCCACTCAGCACTGAGTTAGAGCTGGGTGGGGGCATGTCTGCCTTCACACGCTGCCTTATGGCTTCTGTGTCTCCAACAGCCCTCAGCCTCTGGCTGCTCTCCTTCCCAATAGTCACAAGATTTACCATGATAATAATAGGTTAAGACTTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

Alternative protein isoforms

No structure available
Features
Disorder rate (Iupred):
  C1=0.200 A=NA C2=0.205
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGAAGCCGAGTTTCCCAC
R:
TCCTCCTTAGCTGCCAGTCAT
Band lengths:
357-693
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