GgaINT0124544 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6879632-6881137:-
Coord C1 exon
chr17:6881026-6881137
Coord A exon
chr17:6879708-6881025
Coord C2 exon
chr17:6879632-6879707
Length
1318 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
CTCTTCTGTTCTCCTTGCAGGGA
3' ss Score
13.31
Exon sequences
Seq C1 exon
GCAGCAGCAGTCGCCAGATGCTTTGGAATCGTCACAGTTGGAGGAAGAAGTGGATGAGCTCTCCCTTATTGACCACAGTGAAATTATGGCTAGGTTAACACTGAAGCAAGAG
Seq A exon
GTAGGTTCTTTGGGGTATTGTTCATGTTCTTTGGTTTATATTCCATTGAGAGCTGATTTTCTGAAGGCACGGTTAGCAGGTTTCCCAGACAGGACATTGCATTACTGACGGAGAAGCCAAAGTAAGAATTGACTTTGTTTCTGCCTTGGGTGCATTCCCAGACACCTTTGCTTACTATGCTCTCAACCAAGCTGTTTTTTCATGCAGCTTGAGGGAACACACAACCTTATGAAGCTTTCAGATTTGTCAGGGGCTAATCCTGAACAACAGAAAGAATTCGTCATTTACTGACACTTTAGGAGTGTTCTTTGGGCAGCTGAGAGAGAGAGTGAGAAGCTATTGCTGATTCCATAAGCAGTATCTTGCCACAGGGTCACCTAAATGCACATTTTACACATAGCTGCTCAATGGCTGTAAGTCTTTGGGTTTTTTTCCAGCGTTTTGCATATTAAAATAGCAGGCTCAGATGAGGGAAGCCAGGCACCATTCCAGTCTGACCTGCAGGAATATTTCCATCAACTTTAAAAAAACAACACACAAAACCAGCAGTGACTGCAGATCATTTTGGAGTTGCAGATCTGTGTCAGCCCTTAACTTTTTTCTTCCTTTTTTCTTCCTTTATTGTCTGCATGTTATAAACAGTATAGAACTGCTCCTGCACGCCATTTCCTGCACCGTGGGAACCACTGGCTGACTGATAGATCAGTTCTGCATGTTTTCAGTTGTGAACAGCAGGAGCTAAAAGAAGGATGTTCTCAGAGTGATAAGGCAGGGGTCAAGGAGTTAGCGGGGCTGTTCTTCTGCTCCTGGTTATTGGATTGCTTCAGGTGACCTCCAGCCAAATAGTTCCAGATTAGGGAATTAACTTGCTAGGTTTTTGATGTTCCAGGAGCATGCGAGTTGAATGCACGACCTCTCACCCCGCGGCCACTGTGGTACACGATCCTGCACTTTGAGACAGTTCACACAGAGCTGCTGCTCTGTTAATGGTCTTTTGGGAGCGTTTGGGAGTCTGGGAGATTTCTCTTCATTCTTCTGCGGCCAGAAGGTTCAGCTTTCACTGTGCTTCACAGCCTGGTTGTAAGGAGTCAGAGACCCTAAGTGGTGATCGGCCCAGATCCTCATCTGGGACACCAAATGTTTGGCTCAAATTCCAGGATTAGCCCAGCACTCCGAGATCATGTCCCAGCTTGAGCTGCCAACAGTGCCAGGAACCGTGTGTGCTCTGCCAGTTAGTGCTGAGTTTGAGCCCCAGAGATGGTAAACCAGGCCGAAGGGAGCTTGGATTGTGTGTAAGGCTCTTCTGTTCTCCTTGCAG
Seq C2 exon
GGAGATGATGGGCCAGATGTCCGCGGTGGATCTGGAGATATTTTGTTGGTGCATGCAACAGAGACCGACAGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.640 A=NA C2=0.423
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061815=RasGEF_N=PU(20.0=76.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAGTCGCCAGATGCTTTG
R:
TTTCCTGTCGGTCTCTGTTGC
Band lengths:
182-1500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]