DreINT0124585 @ danRer10
Intron Retention
Gene
ENSDARG00000079872 | rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:ZFIN;Acc:ZDB-GENE-070912-385]
Coordinates
chr9:2974056-2975855:-
Coord C1 exon
chr9:2975734-2975855
Coord A exon
chr9:2974240-2975733
Coord C2 exon
chr9:2974056-2974239
Length
1494 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
CTTGATGTGTTCTGCTGCAGTGG
3' ss Score
6.2
Exon sequences
Seq C1 exon
GCGGAGCTGCATCGGCACTGAGCTCGTTGATTGGCTGTTGCAGCACACATCATGTGTTCACTCTCGTGTTCAGGCTGTAGGGATGTGGCAGGTGCTGCTGGAGGAGGGAGTGCTTAACCACG
Seq A exon
GTAAACCTCATAATACACTAACATACGCCAAAGGTTCAGGGTCAGCACAGTACTGTAGTCAGGGTGCGAATTATACAGTTGAAGTCAGAATTATTAGCCCTCCTGTATTTTATTTTTCTCCAATTTCTGTTTAATGCAGAGCAAATTTTTTTCAACACATTTCTAATCATAATAGTTTTAATAACTCATCTCTAATAACTGTTTCATTTATCTTTGTCATGATGACAGTAAATAATATTTTACTAGAAATACTTCGAGACACTTCTATACAACTTAAAGTGACATTTAACTAGGTTAATTAGGGTAATTAACCGAGTTGAATTGCAAGTATTTGATTAACGATGGTTTGTTCTGTAGACAGTTAAAAAAATATTGCTTAATTGTTAATTTGATTAACAACCTATGAACTGAGAAATACTAATATAATAAAGTTAGATGGCCACCTGAACATCGGGAAGAAGGACGCGGATAACCTATGAACTTTTAAATACTTTATAATAAACAAATAAAGCAAACGGGCGGCAGCTCCTCACAGACACTTCCGTCAAACCGAAAGCAAAAGTAAAACAATATGTCGGGGCCCGGTTCTCTCTCTCCCAGCACTGGCATCTCTCCTCATTTTAGCTTTCAGGGCTCCTCCGTGAGACTCGGGGCAGGGCACTCATCCAGGCAATAGTATCTGGTTGCAGCCTTTATGATGCAAGCTGAGATTGCTTCACTCAGCAATGCAATGTCAGACACAATGCATTCAAATGTAGCGAGTGACGTCACTGTGACGGGTAGTGTTAGGTGAGCCCATTAAAAAGCATTGGATGCAGCCCAGATTGCACTGCACCAGGTCTGCAGCCAGACCCCTTTCCATCCAGGTGTCCCTGATTATGTCACCCACGCCACCTGTCTCGAAAGCCCTCAGGGGTTTCAGCCCAACACGCAACCATCTTCATTCCAGCTGTTCGCTCTTCAGTTTGCGTGAACCTTCACCCTGCTGCTTCACTGACATCAAGTCCTCCAAGCTCATGATGGAGTCAGACACAATATTCATTCTGTCTCCACTGCAGCATGACTTTATATCCTATACTGGACAATATTTCTGTTCAGTGACAAGACTTTTGTCTAAGCAGAGTCAGACCTTACTGTCTTAATTGAATAATTAAAATCAAGGCATGATCAGATTTTATTCTGTAAAATAAGCGTAATCTAGAGGCTTTTACCTTTCATATAAGCCACTTCTGATAGCAAATGATCAACTAGAAGTCAAGTTATTATTTACTGTTCCTAACACTTGGATAGGCGACAAGACTTTTCTCAGGTAATGTATGATTTATCTGTGCTAAATTTAAACAGAAAAGCAGTAATATTCAACTTAATTTGTTTATTTAAATTCAGCCCAGATTAATTTTCTGCAAACACCTTTAAGAAATTGAGTAAACTCAATGCATTTTCAGTGTAGTTGTGATCGTGTGTTTGTTTTCTGCTTGATGTGTTCTGCTGCAG
Seq C2 exon
TGGACCAGGAGCCGACTTTCCAAGATAAATATCTGTTTTATCGCTTTCTGGATGACGAAAGTGAGGATTCAGGAATGCCGAGTGAGGAAGACAAGAAGGAGAGTGACGAAGAGCTGCAGGACACGCTTCTGCTGCTGTCTCAGATCGGCCCTGATGCTCATCTGCGGATGATCCTGCGCAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079872:ENSDART00000144046:8
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=0.194
Domain overlap (PFAM):
C1:
PF0061016=DEP=FE(57.7=100)
A:
NA
C2:
PF0061016=DEP=PD(21.1=24.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGCACTGAGCTCGTTGATT
R:
TGTTTGCGCAGGATCATCCG
Band lengths:
294-1788
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]