DreINT0124474 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11794626-11795068:-
Coord C1 exon
chr8:11794920-11795068
Coord A exon
chr8:11794805-11794919
Coord C2 exon
chr8:11794626-11794804
Length
115 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
ACGTTTTTTGACCACATTAGAGT
3' ss Score
4.57
Exon sequences
Seq C1 exon
TAGAGTCCCAGCGCTCCCACTTGACATCCTTCACCATGAAACTAAAGGACAAATTCCACTCTCCCAAAATCAAGAGGACACCATCAAACAAAAAGTCCAAACCACCACCAGAACAACCCGTAAAGTCCCCAGAGAAAACTGTAACTAAG
Seq A exon
GTATGGAGTAGATTTTTTAGTTGTCTGAAAACATGGCAGGTCTAAAACCAAATAAACATGTAGTTATGTTTTACTTGTCAGTGACATTCTTGGTAACGTTTTTTGACCACATTAG
Seq C2 exon
AGTCTGAGTCGATTAGAGGAGCATGAGAAAGAAGTGGTCAGCGCCTTGCGGTACTTCAAGACCATTATTGACAAGATGGCGGTGGACAAGAAGGTGTTAGAAATGCTTCCTGGTTCTGCTAGTAAAGTTTTGGAGGCTGTCACAGGCTTGGTACAACTAGATAGCAAGATACTGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.869 A=NA C2=0.074
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCTCCCACTTGACATCCTTC
R:
AGCAGAACCAGGAAGCATTTCT
Band lengths:
258-373
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]