GgaINT0049904 @ galGal3
Intron Retention
Gene
ENSGALG00000009357 | RAPGEF4
Description
NA
Coordinates
chr7:18779466-18780904:-
Coord C1 exon
chr7:18780758-18780904
Coord A exon
chr7:18779564-18780757
Coord C2 exon
chr7:18779466-18779563
Length
1194 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
CTTCTGTTTCATGTTTACAGAAA
3' ss Score
9.02
Exon sequences
Seq C1 exon
TTCTGTTTAAGGTGTACTGCATAGACCAAACCTATACCACCATCCGCGTGCCGGTGTCTTCGTCTGTGAAGGAAGTGATCAGCGCAGTAGCAGATAAGCTGGGTTCTGGAGAAGGCCTTATCATAGTAAAGATGAGTTCAGGAGGAG
Seq A exon
GTACTGTATTTCTGTTATGTTAAGTATTTCTCATAGTGAAAGGGAAGCTCAGGAGGGATTGAAAAGCAAGACTAATTCAGTCGTGGCTTTACTACCATATGCATGTTCAGCTAGTACAAGCTATGTCAGAGGCAAGTCCTTTCCTCACTGCAGGCACAGACTGGAGCTCACATGGCATACTGGGAAAATGAGCAGCTTGTGTATCTGCATGTTACAGAGTAGAGCTACCCCAGGTTCCCTTCAGTGTAGGACTTTCCGTTTTTTTAACAGCAGAAATATTAGGTAAACATGGATAATGTCAGTTTAGATGTAAGAATTAGAAGCAGCAAAAAATGCTGCGGTACTGACATTCCCGTATTGGTTCCTGCCAGTCTGACCTCCGTTCAGCATCTTGGTGCCAAGCCCACTGACCTGGTGTTGGCAGAGTCAGGAGTCAGCCCCGTACTGTAGGCTGTAGAAATGGGAGAGTGACCTCAGGGTGGGTTCTGCTGGAGAATTAGTCTTGCTGAAGTGCTCTGGTTGAGTATGATTGTGAGGACACACAGCGCTAATGAGAGCTGTTTCGGAAGGCATTTTTGCAGACAGTGATGCCTGCCAAAAACATTCACTTCCTGAGGACTGACACCAGGCAGCCCTTGTTTTTGCAGTTGCAGCAATTTTTTATTGTCAGATTTGCTGACAGCCAAATCTCTCTCTCTGACAGAGATTTTTCTAAGTTACCTCATTATCTTTTCTTTACCTGCGATGTGATGTTCTTTTAGAACTGCTGTAATGAGATTTGAATACAGTTAGATTTCATCACTTTCTCATGCAGTTGTCTTCCAAGGAAATTTCTAGCAAGAACAGCTCTCCACATGCTTAGAGCTCAGAGAAGAATGAAGATGTAATGATGGCTGTAACAATGGCTAGATTTTTGCTAGTAGTTTCTAGAGATGGCAGTGCAGGCTTCTTAAACTGGCTGTGCAGATCGAGGCTGAGATTCCAGTTCTTGATGCCAGTTCTGAATGAAACTGGCTTGGGCTGAGCTTGTGATGTTTCTTCAACAAAGAGGACCTTATTGCCATCTATTTCTGTCCTGGACCTTGGTAGACTGTGTAAAATTTGTTCCCAGAATGCTAATTTGTGCAGCTATTGAGTCAGTCCTTCTGTCAGTACTACAAATATTTAATAAAGTCTTCTGTTTCATGTTTACAG
Seq C2 exon
AAAAAGTCGTGCTCAAGCCTCATGATGTTTCAGTGTTTACAACTCTCAGTGTTAATGGACGGCTCTTTGCTTGCCCGCGTGACCAGTTTGATTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009357:ENSGALT00000015238:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=FE(61.2=100)
A:
NA
C2:
PF0078818=RA=PD(35.0=84.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGTTTAAGGTGTACTGCATAGACC
R:
TGAATCAAACTGGTCACGCGG
Band lengths:
241-1435
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]