GgaINT0049890 @ galGal3
Intron Retention
Gene
ENSGALG00000009357 | RAPGEF4
Description
NA
Coordinates
chr7:18815040-18816601:-
Coord C1 exon
chr7:18816480-18816601
Coord A exon
chr7:18815224-18816479
Coord C2 exon
chr7:18815040-18815223
Length
1256 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
ATATGTTCTGTTGTTTTCAGTGG
3' ss Score
8.89
Exon sequences
Seq C1 exon
GCAGTGCTGTGTGGGAACAGAACTTGTTGACTGGATGATGCAGCAAAGTACTTGTGTCCATTCACGAAGTCAGGCTGTTGGCATGTGGCAAGTATTGCTGGAAGAAGGTGTTCTTAACCATG
Seq A exon
GTAAGTTGAAGAAATTCAGAGCCTTGACTAAAATTTGGTGAATGTGTCCCATCATTGTCTCTGTGGATTTCTTTCATGAAAAATAAAGGGATCATGAGCCCAAATGAAAAACTACAAATAAACCTCTTCAAAAGTTTGATTTGTATGCAATATACAGATGGTAATAATTGAATCTTGCTACCAACATACCTTTATAACTTATGGAAATATTGAAAAGTCAGTGAAATTGCGATGTTACAGTAGCAACTCTAATTAGACTTATTACACTGATTAGTGATTATATTTCAAAAGCTGGATATCACCTGAACCAAAACCAAGGTATATGTTGCCATACATAAAACTGATCTTCAAGTTAAAAATTTGCAGTGTTTGGAAGCGAATGTAAGCATTTCTGTTTGCTCTTATCCATAATTCTGGGATGATTTTCAGTGGTTTTTGAATGGTTCCCAAATTCTGCTCACCAAATATCCCAGTGCAGAGATCTGTGATTTTATGTTAGTTTTCTGATTCTATTTTACATTGCCTCATGGGTTCCACTTGGCAGGATTTACTAGGTAACTGAATGTTATAGCCCTCTGAAGTGCAGCTTTCTAAAGCAGTATTCATATCTGAAGCTGTGCATGTACAGCTTTATGAAGTTCAGAACAGCAGCACTGCTACAGTACACTTCCAGTCATTGTCTGTTGTGCTTTCCACATCCCAGGGAGAACTTCTCATTCTGAGAAGACAGATTGTTTCCACCGTTTCCTTTCGTAAAAGGCTGTAGCTTACATTCCTGCCTGATACTGTCTTGAATTCCTAGGGCCAAGCTGCTGCAACTGCATCACACTATCCAGCTCAACACACCATTATGACTTGCTTGGAAGACCAAGAGTTTGTCTTTTGCTGTGTCAAAGCCTCTCTTTAGAAGTCTTCCAAGAGAAGACTTACCATTACACTCCCCACTAAGATACAGGTCAATGACCTTCGCTCTGGTATTACATATTGATGATACACATTACTGGAACATGATTTTAGCTGCTTCTTGGTTTGTTACTTTTCAGCCCTCTCTGAAACAGTTAGGGTAAAGTATTCCTGATAAAGTACAACTCCTAGAAATTCTTGATGCAACTGCTTTCTGAGTATGAATTGTTTGCTTAAGTGAAGTGGTTTGAAACGATAAGAACTGAAAAAGGTTTAGTAAGAATTAAGTTAATTTTAAGTTAGTTTACTTTAGAGAGGAGAGAGAAGTGTCTGATATGTTCTGTTGTTTTCAG
Seq C2 exon
TGGACCAGGAACACCACTTTCAGGACAAATACTTATTTTATCGATTTTTGGATGATGAGCGTGAAGATGCCCCTTTGCCAACAGAGGAAGAGAAAAAGGAGTGTGATGAGGAGCTACAGGACACTATGCTGCTTCTGTCCCAGATTGGGCCAGATGCTCATATGAGGATGATTCTCAGAAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009357:ENSGALT00000015238:10
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=0.194
Domain overlap (PFAM):
C1:
PF0061016=DEP=FE(57.7=100)
A:
NA
C2:
PF0061016=DEP=PD(21.1=24.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTGCTGTGTGGGAACA
R:
TTCTGAGAATCATCCTCATATGAGCA
Band lengths:
302-1558
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]