DreINT0124483 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11748633-11750855:-
Coord C1 exon
chr8:11750771-11750855
Coord A exon
chr8:11748728-11750770
Coord C2 exon
chr8:11748633-11748727
Length
2043 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
TGTTTCCTGTTTGTTTGCAGATC
3' ss Score
12.01
Exon sequences
Seq C1 exon
GCCTGGCACATTGCATGACTTCCGTAGCCATGAGATCGCAGACCAGCTGACGCTCCTCGATGCAGAGCTCTTTTATAAGATAGAG
Seq A exon
GTACAGATTCTCCAATATCTTCTTTTTTCCAAGAGATCCCTAATTTAATATTTAAATTCTTTAATCGCCCCTTTAAAAAAAACTAGCAGACCCGTATGCTTTTTATTAATTACAATTACATAAAGATTCAAATAATGTAATTGACAAACGTTCAACTTTAAAGGGGACCTATTATGCAAAAATCACTTTATAAGAGGTTTAAACACAGATGTGTGGCAACAGTGTGTGGATAAATCCAGCCTCTAATGGTCAACATTAGTTAATTAATTCAATTTAATTAACTTTAATTGACATTCTTTGTTTGTACACGTCATCAGAGGGTGAATGAACCACCCATTGGTGATGATCTCCCCTCATCGGCATATTACGTTAGTCTTGTTTTTTGAATCTGCCACTATGCTAACACATAGGCATTTGTAGCTCCTCCCTCTTTTGAAAAAAGCTCAATCTCATTTAAATTTAAAGTGACCATCACCAAAATGGATCTAAGGCAGTTTCGAAGAGTTATAAAACATTTGTGGGGTATTTTTGCTTAAACTTCTAGGGACATCAAAGACTTATTTTTACATCTTGTTAAAAGCATAATAAATCCTCTTTAAATCAACAAAAAAGTTTGATTGATAAATATTAATAAACATTGACTACTAAGATTTACTATGTTAAATTTTTTTAGAACGCAAAATCTGTTTGTTTGTTTGTTTGTTTGTTTTTTTAATCTTCGTTCTGTAGTATTGCATAAAAGCTTAGTCAAACTTTGTTTGGGTCTAAAATAGTTGATACTTTTGAAAAAACATTTAACTTAAGGCTTATTCTCCTGTGGAAACAAAGTGGAAACAAACATCTCCACCTTCATATGACGGATGAATAAATACATTTTTTGTGTTTATATTTGGGAAAAATGAGGTTTACATTAAAAGGGTCTTTAAAATCTTTTTACAAAACATGGAAAACTTTGTTGAATTATATTGACACTTGATCTAAAGCAGAAGAGGAATAAAGCATTTTTACATTAATATTATTATTTATTTATTTCTTTTATTGTTAGTTTTTTTTATTTATATATTTATTTTTTATTATTTTTTACATTTACTGTTATTTAATAACTATATTGTTTTTTTCATTGGTCATTAGTTCTTTGTTGTGAAAAAGCAGAACCGTGCCCCCTGTTTATTTTTTTTTCCCAATTTCTGTTTAACGGAGAGAAGATTTTTTTCAACACATTTCTAATCATAATAGTTTTAATAACTCATTTCTAATAACTGATTCGTTTTATCTTTGCCATGATGACAGTAAATAATATTTTACTAGATTTTTTCAAGACACTTCTATACAGCTTAAAGTGACATGTAAATGCTTAACTAGGTTAATTAAGTTAACTTGGCAGGTTAGGGTAATTAGGCAAGTTATTGTATAAGGATGGTTTGTTTTGTAGACTATCGAAAAAATGCATAGCTCAAAGGGACTAATAATTTTGACCTTAAAATGGCTTTAAAAAAAAATCTAAACTGCTTTTATTCTAGCTGAAATAAAACAAATAAGACAAAAAATAAATTATCAGGCATACTGTGAAAATTTCCTTGCTCTGTTAAACATCATGTGGAAATATTTAAAAAAGAAAAAAAATCAAGGGGGCTAATAATTCTGACTTCGACTGTACATTATATTGTATCTGCACAAAATGTTAATAAATAAATATGGCAAAAAGAAGCTAAGTCGAACTTTCCATTTTGTGTGATCCTGTCTATGGTCTGAACAAAACTGCAGACAGTCTGAATGAAAACGAAAGGACATTCTGTAAGAAGTTTGATTAATGCTGGAAAGTGATTACTGTAGGTTTGCACTCTTTTAATGGTGACATTAACTGTCAATAAATTGTTTTATAATTACAATCTGTTTTATTTTTAACCCCTCAAACTAGAGTGATGCTTTATAAATCTTTTTTTCGCCCCTTAGTCTGGGAGCCATCGCTCTAATATCACACATCAGCCATTTGACTAATAAAGATGGAGTGTTAGCCGACATATGTTTCCTGTTTGTTTGCAG
Seq C2 exon
ATCCCGGAGGTTTTACTTTGGGCAAAAGAACAGAATGAGGAGAAAAGCCCCAACCTGACCCAATTCACAGAGCACTTCAACAACATGTCGTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:18
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=0.091
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=79.3)
A:
NA
C2:
PF0061714=RasGEF=FE(18.0=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]