GgaINT0124546 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6875400-6876848:-
Coord C1 exon
chr17:6876764-6876848
Coord A exon
chr17:6875505-6876763
Coord C2 exon
chr17:6875400-6875504
Length
1259 bp
Sequences
Splice sites
5' ss Seq
CAGATATCC
5' ss Score
-0.27
3' ss Seq
GCCAGCGGTTGATTCTTTAATTT
3' ss Score
-4.84
Exon sequences
Seq C1 exon
ATCTGGTGCTGTACTGTGAAGCCTTCCTGACTACATACAGGACATTTATTACCCCTGAAGAGCTCATCAAGAAGCTGCAGTACAG
Seq A exon
ATATCCTTTTCCATGAAAGGCAGTTCGCCCCAGGGAGCAGAGCAGAGCAGTCGTCATGGAGGGAGCTGGTGGCAAGCAGGCTGGTCACAAACCTGCTGAGAACGTTGTGCTGTGATTGCCCTGGAGGTGCCCCGAGCAGCACTTCCTTCATCTCTGCTACCTACAAATAGGAAATGCCACAGGGCAGGTCTGCGGGGAGCGGAGTGCTGGACCTGAGCGTGGTGTCCTGGGGGCCTGAGAGCAGAGAAGAGCAGTTCAGATGTTCTGTACAGAAGTGGGGAAGTGGTCGTTTGTGTGGGACGTCTGGTCTGTAGAATGGAGATCGTGTGTCCGTCCTTCCAGAGGGGCTGAGGGAATTGCTTGGGCAGATGTAGGTTAACACCAGCGATGGCTGAACTGTCAAATCCTATTCTCCCTCTTATTACAAGAAATGCAACACAGAAGATAATGTCCTCTTAGCCTCCAGCTCTGAGCTTGTATCTGCTAACGAGGCCGGGGCTGGACGTGCAGTGTGAGTGTTAGTGCTCCTGGCAGCACAGAGCAGGCTGCTCGCTGAGCACGCAGTGCTTCCCTTTGGCTCTGTCAATGTCACTCCCTTTGCTGCGTGGGGCAGCGGCCTGGTGGGCTCTGCTCCTGCACACACCCACCACAAAAGCAGCTTGATGTCGCCCTGGCCTGAGCCGCAGCTCGTCACTGCCATCTGCAGCAGGGACAGCCTCCCTCACTCCTGCTGGGATCGGTGCTGCCAAGGACACAGCAGAATCTCCTTGGAGAGCAGGTGTCGGTGGGAGTGTTGGCTGGGGCACTCCTGCAGGCCCTCTTTAATATTTGGCTTGCTGTTTCTTGCACCTGGTGGAAGTCTGCTCAGCCTCTGCCGTCTCCCTTGCTGCCACTCCCCTTGCAGCAAATCGGGCAGAGAGAAAGGTGGAGGTGACATCTGAGATCTGTTACGAGACCTAAGAGATGTCTCACTCTGCCGTGGGAGATGGCAGTAGAGGAATGCAGCTCATTAAATGCCGCCTTAGAGACAATAGACTGGGGGTCCACCTGCCCTGCTAGCATCAGTTCTGCGAGGCATAAGGACCCCCTCACACCCCTGCTGCCTGCAGCTGGTGGCAGCTCAGTGCCATGTTAATTAGAGCCACAGAGGTGTCCTCCATCTCCTAGAAACTCAACACCAGTTTTAGTCAAGGTGGAATAATATCCGTTCTGATGTTCCTCGGGGCAGCTGTTCGTTGTGCCAGCGGTTGATTCTTTAA
Seq C2 exon
TTTGCAACCAACATATGAGAAGTTTTGCCACTTCCCAGACACGTTTAAGAAGCGAGTCAGTAAGAACACCTTCTTCGTGCTGGTGAGAGTGGTGGATGAGCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:17
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:
PF0061815=RasGEF_N=FE(28.0=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(35.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCTGGTGCTGTACTGTGAAGC
R:
CACAGCTCATCCACCACTCTC
Band lengths:
190-1449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]