BtaINT0122344 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32707352-32707771:+
Coord C1 exon
chr5:32707352-32707430
Coord A exon
chr5:32707431-32707620
Coord C2 exon
chr5:32707621-32707771
Length
190 bp
Sequences
Splice sites
5' ss Seq
CCAATATCC
5' ss Score
-12.74
3' ss Seq
TTCCCTTGACTGGGACTCACCTT
3' ss Score
-7.07
Exon sequences
Seq C1 exon
AGACATTCCTCAGTGACTTCCTCCTGACCCACAGTGTCTTCATGCCCACTGCCCAGCTCTGTGCTGCCCTCCTGCACCA
Seq A exon
ATATCCTTCCAGCCCTGGGGGTGAGGATGGTGTGTGGAGCGGGGAGGAGGGATCCCCCGAAGCATGGCTGTACTGATCCCTCCAGGCCCAGCCCATTCATGGGCTCCGGGTGTCCTGCCCTTCCTGTGCCGGTTCCTGAGGGTGGTGGGTGGTCCTGTTGGACACTGTGGTTCCCTTGACTGGGACTCAC
Seq C2 exon
CTTCCACGCGGAGCCCGCCGGGGGCAGCGAGCAGGAGCGCAGCTCCTACATATGCAACAAGAGGCAGCAGATCCTGCGGCTGGTCAGTCAGTGGGTGACCCTGTACGGCCCTACGCTCCGCACCGACCCTGTGGCCACCAGCTTCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:13
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=0.137
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(23.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(45.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATTCCTCAGTGACTTCCTCCT
R:
CTTGAGGAAGCTGGTGGCC
Band lengths:
228-418
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]