BtaINT0122432 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015232 | RAPGEFL1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:HGNC Symbol;Acc:HGNC:17428]
Coordinates
chr19:41116611-41117107:+
Coord C1 exon
chr19:41116611-41116723
Coord A exon
chr19:41116724-41116939
Coord C2 exon
chr19:41116940-41117107
Length
216 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
ACCTTCCGGTCTCTGTCTAGTCT
3' ss Score
8.93
Exon sequences
Seq C1 exon
GATCCCGGAGGAGAGCCAGCCACCCAGCAAGCAGGTGAAGCCACTCTTCCGCCACTTCCATCGGATAGACTCCTGTCTGCAGACCCGCGTGGCTTTCCGGGGTTCTGATGAGA
Seq A exon
GTGAGTGTTCTGGGGGCTCTGAGGGGTCTCCGGATCACCGGCGACCTCTATGGGGTTTCCTTCTGTCTCAGAACCAGTCCTTTTTACAACATCTTTTTCAGAGGCCAGCCCATTTAAGATTGCAGTGGGGTGGGGAACAGAGGTGCTCAGGAGGGGGCTGTGCTGATGCTGCCATTCTGCCCACTGGTGAAAAGCCACCTTCCGGTCTCTGTCTAG
Seq C2 exon
TCTTCTGCCGGGTCTACATGCCTGATCACTCTTACGTGACCATACGCAGCCGCCTCTCAGCATCTGTGCAGGACATCCTGGGCTCTGTGACGGAGAAGTTGCAGTACTCAGAGGAGCCTGCGGGGCGTGAGGATTCCCTCATCCTGGTTGCTGTGGCCTCCTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015232:ENSBTAT00000020265:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.6=5.1)
A:
NA
C2:
PF0078818=RA=FE(71.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGGAGAGCCAGCCAC
R:
CTCCTGAGGAGGCCACAGC
Band lengths:
276-492
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]