DreINT0124478 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11753974-11754986:-
Coord C1 exon
chr8:11754881-11754986
Coord A exon
chr8:11754050-11754880
Coord C2 exon
chr8:11753974-11754049
Length
831 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
TCATAATCTGTGTTTTTCAGAAC
3' ss Score
9.18
Exon sequences
Seq C1 exon
CTGGAAGCAGAAGTGTGTGGACTCAGATTTGACCTCAGAAGAGGTGGATGAGCTCTGTTTGATTGACCACGATGAGATCATGTCTCGCATAACACTAAAGCAAGAG
Seq A exon
GTAAACTTTTGCGTTCGTTATTGCATACAGTATGCACATATACAGTTTTGCTTTTTGAAATGCATAGGTTGTGATGATAGTGAAAGCATTAGTTTTTACTCTGCTGCCATCTGCCTGTGACTTAACGCTATTTCAGTGATGAATTGAAGCGCATATAAAACTCCAATGTCAGGAGAATTAAAAATAGACAAGACCGTTAATAAGTAGACCACTCTACAATAAGACAATATGCGACCCTGGAACACAAAACCAGTCATAAGTGTCAATGTTTGGAGATCAGGTTTTGTACATTATCTAAAAGCTGAATAAAGGAGCTTTCCATTAAAATATGTTTTTTTAGATAGGATATATGGTCAAAATGCAGAATTTTGAAAATCTGGAATATGATGATGCAAATAGATCAAAATGTTGAGAAATTTGCCTTTAAAATTGTCTATTTAAAGTGTTTGGCAATGCATATTACTAATACAAAATTGAGTTGTCATAAAATTACAGTAGGACACTAACAGAACATCTTCATGGAACATGTTCTTTTCTTAATATTAATTTTGGCATAAAAAAAAGATCTATAAATTTGACTTATTCAATATATTTTTGGCTATTGGTGAAAATGTAGCCATGCAACATAAAGGTTTGGTTATCCTGGATCACATATAGGACTATTAAGCAGTAAATAGCCCAACTATATCATGCTTCTCAAAGTCCAACTAGCAAGCCGTCTATTAGTAGATTTTAGAAACATTATTTAGCAAGTTATGTTTAGGAACTGGTTACAGGACGAGCTCTAGCTTTAACCTACGTGATGAAAACCTCATAATCTGTGTTTTTCAG
Seq C2 exon
AACGACGACGGCCCTGATGTTAGAGCGGGATCAGGCGATATTTTATTAGTTCATGCCACTGAAACCGACCGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.154
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061815=RasGEF_N=PU(29.4=76.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAAGCAGAAGTGTGTGGA
R:
CTTTGCGGTCGGTTTCAGTGG
Band lengths:
182-1013
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]