BtaINT0122301 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020791 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:HGNC:4568]
Coordinates
chr11:101733333-101734442:-
Coord C1 exon
chr11:101734354-101734442
Coord A exon
chr11:101733519-101734353
Coord C2 exon
chr11:101733333-101733518
Length
835 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CGTGGCCCTTGGGTCTCTAGCCT
3' ss Score
6.34
Exon sequences
Seq C1 exon
GAGAAGTTCTCACCTTTCGCCGACACATTCAAGAAGCGTGTGAGCAAGAACACGTTCTTCGTGCTGGTGCGGGTGGTGGACGAGCTCTG
Seq A exon
GTGAGTCCTTCTGCCCGCGGGAGGGCAGGCCGCAGGTGTCGGCGTGCAGGCTTCCCCAGAGACCTGAGCCTCCCGTCACATTTCCACCTGCGTCTCCTGGGTCACCTGCCCACTGCCCCGCCCAGGGTCCTGGATAGCTCGCTCCTGCCAGCTTCAGCGTGAGCCCCAGGAGGATGACCTGGCCCCTCAGACCTAGTCGGCCCTGACTTCCTCGTGGGGGCAGTGCCCTCGGCCACCAGCGTCGGGAGGGACCTTCTCGTGCCCTCTGCAGCTGTCCCTGCTCCGCTGAGTGGCACTTGGCCATTTCCCTTCGTTTAACAAACACAGAGCATGAGGTTCCTTTCCTGGGTCCAGAGAGCACCCCCAGCCTTGCCCTCAGGGAGGTGACCTGCTGGGGAGTGACCTCAGTGACCGCGGGGTGGGGCTGGGGCTGGGGCACACTGTGAGGAGGAAGTGCAGGGAGGTTCTGGGGGGTCCGGTCCGCAGAGCCCAGACGGCTTCTTGACCCATCACCCCCACGGGGCCCGGAGCTCCTCCGGGGCAGCATTTGTCTCCAAGCCCAGGCCCAGCATGGCCCCTCGTGCTTGTCCAGTGCTTCCGAGCATCCCCCGAGAGGACAGCAGTTACCTGCCACCATGGGGGCTCTGCCGGCAGGGTGCAGGGTACAAGCAGCCACCCCAAGACCCTCTGCCGCTCCCTTCCCACCAGCAGTTTCCCAGCTCTGCTGCGGGGTGTCCCGTGGCCCTCAGGGTCTTGGGGGCTTCAGGACTGGTGCCAGCAGCCCTTTTCTTGTGCTTGCCTCCTGCTCCTCCCTGCGTGGCCCTTGGGTCTCTAG
Seq C2 exon
CCTGGTAGAGCTGACAGAAGAGATCCTGAAGCTGCTGATGGAGCTGGTCTTCCGCCTGGTGCGCAGCGGGGAGCTCAGCCTAGCACGCGTGCTCCGCAAGAACATTCTGGACAAGGTCGACCAGAAGAAGCTGCTCCGGTGCGCCAACTCTGACCAGCCCCTGGCGGCCCGGGGAGTGGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020791:ENSBTAT00000032663:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(28.4=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(21.6=34.9)
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:
AAGTTCTCACCTTTCGCCGAC
R:
AGGGGCTGGTCAGAGTTGG
Band lengths:
248-1083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development