GgaINT0049894 @ galGal3
Intron Retention
Gene
ENSGALG00000009357 | RAPGEF4
Description
NA
Coordinates
chr7:18801396-18802655:-
Coord C1 exon
chr7:18802579-18802655
Coord A exon
chr7:18801543-18802578
Coord C2 exon
chr7:18801396-18801542
Length
1036 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTT
5' ss Score
8.4
3' ss Seq
AAATGTTTTGCTCTGTGCAGGGT
3' ss Score
7.3
Exon sequences
Seq C1 exon
TATTTAATCAGGGAGAAGAAGGTACTTCTTGGTACATTATCCTAAAGGGATCAGTAAACGTAGTCATTTATGGCAAG
Seq A exon
GTACTTCTTTCAGAATTCTTTCTATATAATTCTTATTATTGAAATTGTAAGAATAAGCTATGAAGAAATGCACTTTAATTTAGAGTAGAATTGCTTATCTGAGGAAACAAATTGAAGATAGTTTTGTTAAGAGATGTTCCAATGGTTTCGTTGATGATGCTTCCAGTTGATTGCTATATCATTTTGGTATACATTACACACATTCTGAGTATAATTCAACACAGTCACATCAGTATCTTTAGGACAGAGTCATTTGCTGGAATTTGGGGAATTGACAGATTTTCATCTCATGGGGTTTTTGTCCTGTAAGTTTTACCACCATCTCCTCTTATATTTGTACCACTGACTCTTATCACAGATGTCAGGTATGTCTGACAAGAGCTGCTCTTGGCTAGGGGTTCTCAGGCTGAATGTGACCCTGCCAAATTTATGTTACCTCTTCATTTTGATTAAGTTTCAGTCTGAAAAGCATCTCTACTGAACTTCCTGTTTATGAGAGAGGTTTTTCCAGGCCTTTGGTACTCAGCAATCCCTTGGGTCTTTAAAAATCCCTGTTTCTCTACTGATTTCTCATTCTGTGAATGAGAGTTCACACCAAGCATTTCACCAAAATCTTGCACAGGGGCTAGTGAATTTTACAGAGGGCGAGCCAGATCATCTGTTACTGTACATTCAAGTAAATGGCTTTGCACTATCTGAAGATGTGATGTTACGTGTTGCAAATTCAATTTTCTTTTTCAGTGACTCCTTAAGCAAAGCAAGGAACATCAATCTGTCTTGAGAAGGGCTAGAAGAGTCCTTCATGCTGAATGTAATTTCGGAGAACAATCCAGTTCTTTTCTATTCTTGTCTTTCTTTAGTAATAGTAATAGCCAGTTATCAAGTATTGTTTTCTAGTCATTATTTTGGCTGTTGATTTCCTGCCAAATACATTTGTTTTGGTATTTGATTGTGAAGCCCGGTGTTTGTATAAGGTTTTTCAATAGAATCCACAGTAACGATGGGTTTCTGCATGTAAATGTTTTGCTCTGTGCAG
Seq C2 exon
GGTGTGGTATGTACTCTACATGAAGGAGATGATTTTGGCAAGCTAGCACTTGTGAATGATGCTCCCAGAGCAGCATCTATTGTTCTACGTGAAGACAACTGCCACTTCTTGAGAGTAGACAAAGAGGACTTCAACAGAATCCTTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009357:ENSGALT00000015238:14
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:
PF0002724=cNMP_binding=FE(28.7=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(55.2=100)
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:
ACTTCTTGGTACATTATCCTAAAGGG
R:
CCTAAGGATTCTGTTGAAGTCCTCT
Band lengths:
201-1237
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]