GgaINT0124542 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6882417-6884169:-
Coord C1 exon
chr17:6884077-6884169
Coord A exon
chr17:6882506-6884076
Coord C2 exon
chr17:6882417-6882505
Length
1571 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
AAACTTCCTTCTCTTTGCAGGAA
3' ss Score
11.5
Exon sequences
Seq C1 exon
AGTGAAAACGCCAGTGAGGAGGCTGGTGAGGGTGAATACGTCAATCTGTATTCCTCTGGCCAGAGCAACGGGGAACTCCCTCATTCTGGAGGA
Seq A exon
GTAAGTAACCGGGAGAGGCCACGCACTGGGAAGGGGCTGCCTGGTGCATGCTGAGCTCACACTGTGGCCCGGCCCCTGTGCACCCCGGGGTGCCCGGTCCCCTCGCTGGTGGTCCCTTTGCTTGCCCTCTCCTGGCTTGCAGGCTTTGGTGGCCTCCTGTTCTGCTGCTGAGAGCCCCAGCAGGACGGAGGGATGGCTTTGCCTTCCTCCTGGCCCGTTTGTGCTTTGCTGTTTGTCTGGAGCTGCTTGCATAAGGTTCCCTTTTGGAGAGCTGCACTCTGGCCAGCACGGTCTTCTGTCTGTATTTACTCTTGTAACCGCTTTGGCTTTCCTATTTCAATAAGGCCTTGTACTCCCCTTTTTTAATTCTTATTTTTCCTTCCCCACTTGGGTATGAAATGATTGATCAACAGCACTGTAACCACGCACTTTCTTCCTTCGCTCCAGCCTCCTGTCCGAGCTGTTCCCTTGGGATGGGGTGTACCCCATGGCAGGGAGGTGCCACCTTCCTGCTGTGTCACCGCAGAGCTCTGTGCTGCTCTTTTTGCCAGCCCTCACCTGGGGCGGCCCATCTGCAGGATGTTTCCAAAGCCTTTATCCCTGCTGGCCTTAAATATCCGAGGAGAGGGTGCTGCCATCACTCCCCTCCATGAGGCAGCCCCAGCCTCACAGCAGTCACTGACTGATTCTTAACTTGGAAGCAAAGGTCTTTACAGATAGCTGCAGCCTGGAGTAATTTACAGACACTGACAAATCTCAGCTCCCCCGTGCACCTTCCCCACCAAAGCTGGGCAGAGTGGAGGTGCTTTCAGTCCTGTCTGTTCAGTAGATGGAATGTCCAAGGTCCACTTTGCATGATGTCAGATAATTCTGAACTCCAGCACTGCTAGATTAATGTCCCCATTTGCCATTCATGGCTGTTTCCCTCTTTAATAAATGGCTAATTTAAAGTGCTGCAGCTCTATTTGCTCTGAGCTGTCCACCTGCTGTTCCATGCTGTGTTTGGATGGTTCTGCTTGTTTGCATTAGCCTCATTTCCACAGCCATGAATTGTGAAGTGGAAAAGTTCCATCATTGTGTGAGCTCTTCTGATGGAGGAGAAGGGAGCAGGAAAGGTACTTTGCATCCCCCCCCCCCCCACCTCCAAGGCAGTCTGGTCTTTTGGGGGCTGTAACTGAGAGGGGAACTGAAACTGGAGAGCTTGGAGCTGGCTGTGTCCATTCTGATTAAAGCAGAAGGCAAATGTATTTCAACAGTAAGGGCTGGAAAAAAAGAGCAATGAGAGGGTTAAAATTCAAGACAACAGCTGACTTGTGTTGTAACTTTCAGCATCATTTCACAATGTTAAAAGCAAACAATACTAATTACACTAGTCTCCAGAGATAGTCCCAAATTTCCTATCTAATTAACTTCTGTGTTTTCCTGGCATTTGGCATTAACTTGCATCAATCTTTAACTGCTCTGAAGGAATTTACAGTAAAGAGCCGTTTAGAGGCAGTAAGACTGTAAATGCAAGCTTGGCTGTGGTGCAGGATTCAGGGCAATAACGAAAAACTTCCTTCTCTTTGCAG
Seq C2 exon
GAATCTCCCTCTGTCAAAGACGGCCATTCCAAAGACTCCACTTCAAACAGCAGTGCCATGGGGAAGGAAGGCAAAGATGGTGCTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGTGAAAACGCCAGTGAGGAG
R:
CTCTCAGCACCATCTTTGCCT
Band lengths:
182-1753
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]