GgaINT0124541 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6884077-6885544:-
Coord C1 exon
chr17:6885263-6885544
Coord A exon
chr17:6884170-6885262
Coord C2 exon
chr17:6884077-6884169
Length
1093 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGA
5' ss Score
8.51
3' ss Seq
TTTCATCCTGTCTCCCCTAGAGT
3' ss Score
10.86
Exon sequences
Seq C1 exon
TACAAGTCTGTGTTTAGGTCCTACTCGCAGGACTTTGTGCCTCACAACCAGGTCTCCGTACCTCCTTTCCTGTCTTCTACCTCCTCCTCCTGCTCCACCGCGCCCTTTCCGCCCGTCCACCCGTCTCCGAGCTCTGACCTCGCAGTGCCAGCCACGGCCAGCCCGTCTCCCAGCACTGGGGATGTGCCAAACTCCTCTTCGCAGGAGAGCAGCTTTAACGGGAGTGCTCCTGTCTGCCTTCCTTCTGAAACCTCTCTCACTGATTCTCTGCAGACGCCTTCG
Seq A exon
GTGAGACTATCCAAAGAGGTGATCGTGTGCACCTTAACGCAAGGCCGGGCTTGTTTTTGCTTTAAAGAAATGTCACTTGTGTTAATACTTGCGATTTGGTGTGAATGCGGAGAGGTGGTTCTGTCCAAAAGCCACGGCTATAAATCTGAGCAACCCCACAGGTTTGAGAGGTTGGAAACGTAAAATGTCAAATGCTGGTGAAGGGGAGAGGAAGAGAAGTTGCTGCTGCTTCCTGCAATTGTGCTACAGATCAGAGGAAGGTAAAGGAGTGCTTGGTGAGGTTGCTTCCCAGCAGTGCTTCACATCCTGCAGGAGCTGCATCCCTGCTCTCCTGCTCCCCGAGCCCCTGGTGAGCCCTGTGAGCAGTGGGTTCGCTCAGCTCCACGCTCCTTATGTAAGCCATTACTTTCTGTGGGCTTCTGCTGTCCCCAGCTGCCGGCGCTGGTGGCGCTCAGTGCAGAGCGTAACGCAGTGCTGGAGCTGGGCTGAAAGCTGTTCCCACACTGACCAGCTCAGGGTCCCTGGTTGGTTTAGCACACCAGTAGGCAGCTTACTTCTTTAAGTACCTCATTTACGAGGCAGTTTCTCGTCTGTGTGTTGCAAAACCGAGAGTTGATGGGATCAGAGCCTCAACTCTGCCTCTTCACAATACTTAGAGGAGGGACGTACGCCACAGAAATCAGGTTTTCACCCTTTAGACCTGACCTCGCTGTTGCATCTTCGTTGCCTCGGGTGTTTGTAAGCACCCAGCAGCCCTCAAGTCTGGCTCAGCCTGGCTCCCCGGGGCTGGCATTGGCAGAATGGCGCTTGTGCTCAGGCTCTGAACGCTTAACAGCTGCACGCTGGAAGTCCTCACTGTGCACCCACACAGCTCCCGTGGCAGCTCTCGCTACGCAGTGCCTGCTGCTGTCCTACTGCAGCTCAGGGCCTTCAGGACGGTCCTTGGGAACTCCGGTATGGCCACCTTTGGGAGCGTGCAGCTGGAGGATGGGCTCCCACCTCGGTGACGGCACCGCAGGGCACAAATGCTTGCTACCAGCCAACGCTGCCGAGGGACACCGTCACGTATTTCCTTTCATCCTGTCTCCCCTAG
Seq C2 exon
AGTGAAAACGCCAGTGAGGAGGCTGGTGAGGGTGAATACGTCAATCTGTATTCCTCTGGCCAGAGCAACGGGGAACTCCCTCATTCTGGAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.723 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
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTACTCGCAGGACTTTGTGC
R:
GGAGTTCCCCGTTGCTCTG
Band lengths:
342-1435
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]