GgaINT0049903 @ galGal3
Intron Retention
Gene
ENSGALG00000009357 | RAPGEF4
Description
NA
Coordinates
chr7:18780758-18782756:-
Coord C1 exon
chr7:18782678-18782756
Coord A exon
chr7:18780905-18782677
Coord C2 exon
chr7:18780758-18780904
Length
1773 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GCGGAATGTTTTTTCTCTAGTTC
3' ss Score
5.67
Exon sequences
Seq C1 exon
CACAAAGTTCTCCTGCAGCTGTTTAATACAAGTGATGACAGAGCACAGAAACGCCAACCCATCAGGGGCAGCGATGAAG
Seq A exon
GTGAGTTCCTTCTCTGAAGAGTTTTCTTGAGCCACTGGGATTTGCAGCAAAGTTGTCTCTCTGAAAGCAAAGGGTCTGAAAATAAACAAAAGTACCAACAGTTTGGAAGCCTGACCTAAAGCAAACTTTGCATTTTCTGAACCAACATTCTCCATCGTTGCCTTGAAATACTCCTGATCTTCTCCCATCTGTGTGCTATAAAGCACTGTGCTTCCTCAGAGGAAGAATGTAGCAACCTTTAAAACAGGGAATGGACAAAACAGGCAAGAACCAGTACAGACAGCGTCCATGCAGGTAGTGTCAGTGCAATAAATATTTGGTGCTGAAGGTCATATTTGAGTCCCTGTCTCTTCTGTGTAGTTTGAGCTGATACGTACAGCTGTTTCACCAGAAATGCTCCTTTGTGAGATGTGAGTGGAGCAGATAATCATGCCCTGGAGCTCTGCCGTGTGGCACGCAGCCTAGAAAACAGAATCTGCTCTTTTGCCCTATTGGTATTGTTTGAATCTGTGGAGAGATCAAGGTAAAATTTACAGCAGTGTGTTAGACTGTCATTTTCAGTTGTGCTGGCTTTTCATGTTGTCATTCACTTCAGGAAGGAAGAAGCACTTCTATATAACAACATCCTGAGATCTGTCCATTGTAAACCAAAACATATGTTCTTTAAAACTAATATATCTGAGGATTTCTTTGCAGCTGCCAGGGCCAGTCCCTCAGTGGTTCTGGTGTATCTTCATCACAAAAAATACCTTCTGCTTCAGAGCGTTTGAACTTAAGGGATAGTTCTTGCTACTACACAGTGGTAAAAATAAGGGAACAAAATGCAAAATCATTTATCTGAGAAAGCCAGTGGCATTTCAAAAGCAGGAGGTAACTGTATATAAACAGCAGAAATCCTGCCATGCATCTGGCAGGATGACTTCTAGGTCTACAAAGAGCAAAGTAGTTTCTACAGCCCCAAAAGTACTACTTCTGTCTGTATGGGCAGAAATTAACTGCTGCTTTCATATGACTGTACCTTTCTCATTCATAGTGCTGGCATCAAACTGAGCCTTGAAAATAGGTAGACAACCATAACCCATGAGACTGCTTAGCTTGGCTTGATGGCTCAGCTGAGAGAGTATTTTGCTAACTTATTCTGTCTTAAATTCATGTCACTCCATGCTGCCTTCCTTTTTTCAGCCTAATGTTCTGTTGTATTGATTCCTAGGCAGCCAGAGACCTACATTCATGTATAAGAATGTGAGCCAATGTGTACTGTACAATCAAGTTTTAGGGAATTTTTCTTCATTGTCTACAGTATTCCTGAATCAGCAATTACATACTTGCCTGTAAAAAAAAGACTGTAGTACAGTTTTAGTTCTGATTGTAACCTGAACTTTATTTTCAAACCTGTTTTGTGAAGTGAAAAGTATTTTCCTGTAATTAAGAGAGTTTGCAGCCAGTTTTTCTGGCTCCTGAATGCAGTTGTTTTTTTTAAATATTATATTATCTGGGACATAATTAAAGTACCGGATGAAACTGGCATCCATAAATAGCATAGCAGTACTAAAATAGTAGTACTTCGTGTTTTACTAAAAGCTCTGGGAAGTCAGAGATTTCTAGGCTAGAAATTGTAGAACATTTGAGGAATGGGGAATTATCAAAACAGTATTTATTTTTGCTTTTGTTCTTTCATTTGTGAGCAGTGGTTACTGAAGTGAAAGTAGTTTGCACAATAACATCTCTGTGACTGTTACATGTGACGTACATAGCGGAATGTTTTTTCTCTAG
Seq C2 exon
TTCTGTTTAAGGTGTACTGCATAGACCAAACCTATACCACCATCCGCGTGCCGGTGTCTTCGTCTGTGAAGGAAGTGATCAGCGCAGTAGCAGATAAGCTGGGTTCTGGAGAAGGCCTTATCATAGTAAAGATGAGTTCAGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009357:ENSGALT00000015238:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=FE(61.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAAGTTCTCCTGCAGCTGT
R:
CTCCTCCTGAACTCATCTTTACT
Band lengths:
225-1998
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]