GgaINT0124539 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6893796-6896050:-
Coord C1 exon
chr17:6895848-6896050
Coord A exon
chr17:6893955-6895847
Coord C2 exon
chr17:6893796-6893954
Length
1893 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTTTCTCCCTCCCTGTTCAGCAG
3' ss Score
10.12
Exon sequences
Seq C1 exon
TGATGGCGTACATGCAGTTTGTAGAGGACTACTCGGAGCCACAGCCATCTATGTTCTACCAGACCCCTCAGAACGAGCACATCTACCAGCAGAAGAACAAGCACCTCATGGAGGTCTACGGCTTCAACGACTCCTTTATCAGCTTAGACCCTTCTCAAGATCTGGCCCCCCCTCCTGCTCTCCCACCGAAGCAGCGACAGCTG
Seq A exon
GTGAGTGACACCGCAGTGCCCTTCCCAGCCCCTCCTGGAGCAGCTGTGTGTTTGCTGCTCCTGTTTCTGACAGGCTGTGGTTGTGGGAGGGGGTCTCACTGATGTTCACGTTGTGTTCCTTGCCATCTCGTTAACATGTTTTTAGGCATTTTGCATCGTCTACTTGGAGCCCTTCTGTTCCTTCCTAACCCCGTGTTCAGACTCTTCCCCTAAAAATGAGATGTTCGTCTTCCACGTGGCATGGCTGAATCTGTGCCAGAATAGAGACGCATGTCATGTCTGTTACTTTGAAGGTTTTGACACACTGAGCAGCACGATTATCAAGAGGTTGCTGCACTGTTGTTCCCAGTGTTGTTTTGCAACTGTTGTCAAGGATGCCACTGATGATAACCATTAAAACGTAATCACTGCTTTTATGGCTCAGTCTGTGCCGGAGCCACAGAACTTTGGTACAGCTATTATTTAACTCCTGCATGTTTTTCCTATGTTAGTCCACATGTGTGATTCAGGAGTTCACCTGGTTTTCACTGCTGCCTAACTTAGATTGGCCATGGCTGCAACAAAACAGGACGAAATGCAGGAGCAGAGCCGTGCTCTTGCCATCATGATGGCAACTGCCGCAGTACATCCTCATGTTATCTGTGCTAAAGTTTGACTGCCCCAGTGTTACTTTGCAATCAGATAGGAGAAGCTACACAGAGGTCTAATTTGGGAATTCAGTAACTACATTCCTGTGGCACAGGTAGGTGTCCTGACAAGATAAAGTAACGTTTCTGGTGAAGTAAACTGAAGTAAACTGAGTATTGTGCAGTTTGTCAGTGGAAGCAAAGCATATCTTTGCTGCCCTTTAATCATTATCTGGGCAGCCAAGATGTCACCATTCTGCCTGTCAGGTATCCTTCTAGCCTTGCAAGCTGATGCTATCAAGGTGTTGCTTGCAGTTCCCCTGAAGCAGAGGTTTCTTTGTGCCTTTGCCTTCATCTCTAGTTGGGAACATGGTGCAAGCAGAGAATGGCTCATTCAGAAATCACTGGAAAAGCCATCAGGTCCTATTGTTCTTCTGCTCCCACTGCCCTGAGAGATTCTGAAGCAGCGAATCATGGAGACATCAGCTGCTCCAGCAGTGGGGAAGTCTGCTGGATGGACTCCTAAAATAATAATTAGGAAGTCCGTTCTTGCAAGCTTCATAGCTTATATGTGAAATTATATGTTATATTCAACAGGACAGGGCTGAGAAAGCCTAGATACAGCTTGACCTCCCTCAGGCCCTTACTGTAATGGAGTTCAGGAGAAATTCCTGGTAGTATTTGTTATTTACAGAGTAATAACTCCCTCCTGTGCAAATGATCTGTCATTTTGAATTGGACTGACAATTTGCTGGGCGTCCTGTTAAGCAGTGTCCCAGCAGCACCTGTGAAGGCCTACAGGCCACACTGATCGGTCTCAAGTTTCCAATCTGCAAATGGACCAAAAAAACAAAACCACAAAAAACTGCTGATCTGCTGGAGTCAGCTGCTGCCCAGCTGAAAGGGGCAGCTCCTTGCTGGGCAGCTGCTCCTGCCCATACCTGCTGCTTTGGGCATCTGCCCTTGGTGTCATGGAGAAGAAGGGCAGTGAGGAACAGCAGCGTGCCTCCCCCAGCCACAGCTGTCCTGGGCTGTTTATTTTTAAGGGATTTGTGAAACAAAGAAGATCTGAACTGTGGTTTTTGACACACCCCTTGAGCTCAAGAAAGGCACGTCTGGCTCTGATGAACTGTATGAATAGCTGTTTGCTTAACAAGCCATTATATGCGTTGTTTTACAGTTAGCGTTTCTTATCCTTTATTCATAGCCTTTTCTGTGCTTTCTTTCTCTGTTTCTCCTGTCTCTTGCTTTCTCCCTCCCTGTTCAG
Seq C2 exon
CAGGCCTCCTATGCTGCCTCTTCTTTCCCTTCTGTCTCCTACTGTGTCCAGCAAACTAAAGTGCCCTTCACCCCCGAGGACACCGGTGCCGCTCAGGGCCTCACTATGTCAGTCTCTAACTCCTTTCTCAACCGGCACAGCTCCTTTCCTGTGCATTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.613 A=NA C2=0.341
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATGGCGTACATGCAGTTTGT
R:
CTGTGCCGGTTGAGAAAGGAG
Band lengths:
343-2236
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]