DreINT0124481 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11750932-11751885:-
Coord C1 exon
chr8:11751793-11751885
Coord A exon
chr8:11751118-11751792
Coord C2 exon
chr8:11750932-11751117
Length
675 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
GTTTTTGTGTGTGTAAACAGTTT
3' ss Score
7.52
Exon sequences
Seq C1 exon
GTACACCAGATTTTCTCTCAGCTCTGACAGCATCAAACAACGAGCTAGTAAAAACACCTTCTTCGTGCTGGTGCGTGTCGTGGATGAGCTTTG
Seq A exon
GTGAGCTGAAACTCTTTACAATCACAGTTGAAAGGCAAATTTATCACTTGTGCAAGCTGTTGAAATGCCTCTGTTGAGCTTTTTTGACTATTGTCTTTTATGAACTATGTAATAGAACGTATTTCGTCACCATGGAATTATAAGGTTTTATCTGACATTTTTGTCAAAATTGAATTATTGACATATTCTTATCAATTGACTACTTATTTACATTATGGGATGTTTTTTTTTTATATAAATCGTTAACATTTTAAGACTTTTTATTTAATATCTCAATATATATTTATTTTAATATCTCAAAATCATTCAGAACGCAGATAGAACCTTATAATTCCAAGGTGACGGTTTGTTTTTTACAATAGGAAAATTGTTGACTACTTAGGGTCAATTTCTTGATTTATTTGACAAATCTATAACTCAAGAGCAATCCAGTGACCCCTCTGAGGTTTCAGTTATATGCCTTTTTTAGTTTTGATTGTAGTTTTGAAGTAATAACAAAAAAAAGCGAATAAAAATCTGGAGAAAATATATATATATTATGAGAAATATTGCTAAATAGCATTGAATATTGCATATTTTTCCAGTATTGTGCAGCCTTATTTTAGAATAAGGTTGATAATTGTTGCTGATGATGTTTTATATTTGCTTATCAACTGTTTTTGTGTGTGTAAACAG
Seq C2 exon
TTTGGTGGAGCTGACGGAAGACATCCTGAAGCAGCTCATGGAGCTTGTGTTCAATCTCTTGTGTAAAGGGGAGCTTACTTTGGCCCGGGTTCTGCGCAAAAACATCCTGGATAAAGTCCAGCAGAAGAAGTTGCTGCAGTACACTAATTCCCTCAAAACACTGGCTGCACGCGGTGTGGCCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:16
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(27.4=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(29.2=52.4)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACCAGATTTTCTCTCAGCTCTG
R:
CGTGCAGCCAGTGTTTTGAGG
Band lengths:
262-937
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]