GgaINT0049895 @ galGal3
Intron Retention
Gene
ENSGALG00000009357 | RAPGEF4
Description
NA
Coordinates
chr7:18800536-18801542:-
Coord C1 exon
chr7:18801396-18801542
Coord A exon
chr7:18800652-18801395
Coord C2 exon
chr7:18800536-18800651
Length
744 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
AATATTAACTTGTCTTGCAGGAC
3' ss Score
8.62
Exon sequences
Seq C1 exon
GGTGTGGTATGTACTCTACATGAAGGAGATGATTTTGGCAAGCTAGCACTTGTGAATGATGCTCCCAGAGCAGCATCTATTGTTCTACGTGAAGACAACTGCCACTTCTTGAGAGTAGACAAAGAGGACTTCAACAGAATCCTTAGG
Seq A exon
GTGAGTGTGGAAAGGTCTGTTCTGGCAGTGTGATGTCAGAACAAAATCTTTCTCGATTTTATCTTATTTTCATGGATATATTCATATCAGTAACCATGTTTGAACCGTTCTCTAATTACAGAGCAGAGATGAGGCGATCTAGAAAATTAGGTAAAGAATAATATTTTTTCCTGCTTTTTGGCTCCTAGCTCAGCCATGAAAACAGAAGCAATTGGACTCTTTGTCTCTCACATGCTTGTATTCTAGAATTTGGTTAGTGCTCAGTTTGTCCTCGATTCCAAAAAGATCTCCCATCCAAATAGTGAATAAAACAACATCTTATCTCTCAGATAGGTCAGTGGCATGTGCCCTAAACTCTATAGGTTCAAGGCAGAATCAAGTGGCAAATGTACTAACTTACAGGTAAATGCGCAGATGTCTTTACCATAGGTCTCTGAAAAGATATTCCCAACTTAATTTTACAGTCATTAAAGTCAGAGCAAATATATTCCAAAATTCAGCTGTATTTCTGTAACTGAAAGCTGCAACCCAATACAAGCTGTATCATTCATAGTATAGAAAGTAAAACATGGTATCATCCTGTGTTGGAATTAAAGCATGCCTAATAATTCAGCAATTAAATCAGCCCAAACAGTACTGTGCTAGAAGAATGATACATGATTGTGTTTGAGTCGTGCACTTTTTCAGAGTAACTTATCAGCCAAATTGGTGTGATTGCTTTCTTAATATTAACTTGTCTTGCAG
Seq C2 exon
GACGTGGAAGCAAATACTGTAAGACTCAAAGAACATGACCAGGATGTCTTGGTGTTGGAGAAGATCCCAGCAGGAAACAGAGTTTCTAATCAAGGAAGTTCACAGCCTCAGCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009357:ENSGALT00000015238:15
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=0.224
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(55.2=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.3=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTACTCTACATGAAGGAGATGATT
R:
TTGTGCTGAGGCTGTGAACTT
Band lengths:
254-998
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]