BtaINT0122298 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020791 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:HGNC:4568]
Coordinates
chr11:101739241-101740939:-
Coord C1 exon
chr11:101740831-101740939
Coord A exon
chr11:101739317-101740830
Coord C2 exon
chr11:101739241-101739316
Length
1514 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
CCTCTGCTGTGCTCCTGCAGGGC
3' ss Score
11.36
Exon sequences
Seq C1 exon
GGCCCGGAAGTCACCAGACGCTCCAGAGGCTCAGTCAGAGGAGGAGGTGGACGAGCTCTCCCTCATCGACCACAACGAGATCATGGCGAGGCTGACCCTCAAGCAAGAG
Seq A exon
GTGGGTTCCTCACAGGCCGTACATGCAGCGTCTGGCCCAGAGAGAGGGTGAAGGGGTGTTGAGAAGGGAACCTGGAAGTGACCCACACAGAAAGGCTGCAGCCAAGTGCTGACCCCCGGTGGCCCTGGGCTGTGGGCTCTGCACCCTCTTGTCCTGGCCCCGTGCCTGGGCCACTGTAGGTGCTCCAGGACCCTGGGCACACTGGCGACTGCCCAGAGGAAGTGTGCTGTCCCTTCTCCGACACTTGGCGAGTGAGCTTGGGCAAGTGGCCTGTCCTCCATAAGCCCCAGACGATGGGACTCTGGAGGCTGTGGTGAGAACGAAGCCCACGTGGGTGCTCAGCATGGAGCCCTGTGTGCTGGGCCCTCCTTAGTTCAGGGTGTTTTCATGTTAGTGACAGAACCGTCCACATGGCTCTCTCTGCGGGGGAGGCACACGCCGATGAAGGGATTTCAGGCCTGGCCACACGGCTGCCTCCAGCCTGTGTCTTATCAGAAGAGCTTCACTGGTGAACATAGTGCCCAAACCTGTCACCGCCCAAGGAGCTGAGCTGAGAGGGCCTTCCACTCCCTGCTGCCCAGCAACCCTGGGGACTCGGGGGAGCAGCTCCCAGTGACGGCCTTGACCCCTCCCCGGGGAGGTAGCCTGTTCTACACACGTGTTCTCCGTGACAGACATGGCCTTGTCATGGCCTGGAGGAACCAAAAGGTGGGGGCTGGCTCCTCTGCAGAGAGAATGATGTGACTTGCCAGAAGTTTCTTAAGAAAAAGCAGGTCTTGGGCGTCACTGCCCTGCCTTAGCTAGAAATCCAGGATGCTCCCAGGGCCCTGGGTTTCCAGGGATAAAGCCTGCCCTAGAGAGGAAGCCGCGTCTCTGAGGGCGAGTGCTGGAGACACGCGGAGGCACGCGCTGGGCGGTCTCCTTCAGGATTACAGGGAGTAGCCTGGGCCTTCTGGTCCTGTGACAGCTCTTTCTTGGCTCCAGGCCAGGTTTATGGGTGAACGCCTCCGTTTGCTCCTAGGAAAATAAGACTTTTCCCTTAATAGACAGGCTGCGGTCAGTATAAGCCACACTGGCTATAACTCAGCATCTTTGTGACGTATCTCACTCCTCTAAGGGCTCCTGGGAAGAACGTGTGTCCCTCCCCCAGAGAGCAGGTGTGGGTTCGGCAGCTTGCTGCAGCTCTCCTGGAAGCAGCCTGCCGTCTGCACCCTCGTCCTGCACCCTCCAGTCCTGCCTGCCTCCCTGTGGGCTCCCCCGTCCCCTCCTCCGCTCTCTAACCCGTGGGCTGGAGGACTGTTGGGAGCCAGGTCCCCGACCTGGCAGTGTCCTCGGTGCCCGGTGCCGTCTGTGGAGCGTGCGGGTCGGATGAGCACCCTGGCCTCTGCAGCTGGGCCGGGCCGCTCCCGGAGCATGGGGGTGCCGTGAGGACCTGGGGGGTCTGTCAGCTCGTCCCTAAACCGACTCTCACGGCTGTACTCTGCCCCATGCCCTCCTCTGCTGTGCTCCTGCAG
Seq C2 exon
GGCGATGACGGGCCAGACGTCCGTGGAGGGTCGGGCGACATCCTCCTCGTCCATGCCACGGAGACGGACCGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020791:ENSBTAT00000032663:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.757 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061815=RasGEF_N=PU(19.6=76.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCCGGAAGTCACCAGA
R:
CTTTCCGGTCCGTCTCCGT
Band lengths:
185-1699
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development