DreINT0124615 @ danRer10
Intron Retention
Gene
ENSDARG00000074307 | rapgef5b
Description
Rap guanine nucleotide exchange factor (GEF) 5b [Source:ZFIN;Acc:ZDB-GENE-061215-2]
Coordinates
chr16:19337901-19339487:+
Coord C1 exon
chr16:19337901-19338079
Coord A exon
chr16:19338080-19339396
Coord C2 exon
chr16:19339397-19339487
Length
1317 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TTTCTCTCCCTCTTTCATAGCTG
3' ss Score
10.05
Exon sequences
Seq C1 exon
CAAGAGTTGGTGTATTTTACTCTGAGTCGTGACTCAAGTTCTGGCCACACGGTGGCGCTGGAGCAGCTGTTGCAACGCTGCAATGAGACTCAGCAGTGGGTGATGACTGAAGTCCTTCTGTGTTCAACCCTCTGTAAACGAGTGCAGCTCTTCAAGAAGTTCATCAAGATCGCAGCACA
Seq A exon
GTAAGTATACGTGAAGAAAAGCACATTTGCTGACTGAAACTACAATGTGTGCATGTCAATCAGCTAGTTCAGCGGTATTGAATTTGCATTAAGAAGATATGAACATCTAAAGCTTGCAGTTGGTCACATTTGCCCAAATGGATCAATGATTTCTTTTTGACATAACCTCATAGTTCAGTTTCCCATTTTATCTTCTGACCAATCCAATGCTCTCTAGTGTCTGACATGTCCCGCCCCTTCAAGATGGTTGTCATTTGCTACTCTCACTGACAGAGCTGCTATTAGTGTTGTTTAAAAGAGGAGGAACTACTACCTGCTACGCCCTGTTTTTATGTTTTAGTTGAGATTTAGGCCCATTCCCAATTCTAACCCCTAGCCCTTCCCCTAACCCAATTGTCCCAATTCTCTTTAGCTTGAAATCAAGGGGTAAGAAATTTTACAAGTATACACCAGCTACAACAGCAAAATGGCTGCACACGGAAGGCAGGAGATGCACAAATTTTTTGACATTATTACAGATTTTAACAACAAACAAGCCTATATTTTAATATATCCATAACCACGTTCTGGTTTTACCGTCATGCTTTTAAAAAACTCGCTAAAATAAAAACCACTACATTTCATAATTTAAAATCCAGAATTATAACTCCTGTATAGCAGTCCCATAGCATTCTAACACTCGACTACCCTGTCAGAAAGGTCTAGTGGCTGGGAATGACCTTTTTACATTGTCTGCTATAATGTTAATGTTGTTTTCGTGTGTTTACATAGATGACTATGTCCACAGTGTAAACGCACTTTAACTTTACAGTTACAAACTTATTGCCACATTATAACTTTTTTGCTATCATGATATTGTTGCCTTCAGTGGTTTCCTGAAGATAAATACCAAAAAATAGCACAACTGGAATAACTACAGTAGTTGCAATCATCTATTTCATATCTGTTTCTCTTGAAAAACGCTGTTTTAAGGGCCAAGGGGAATGAATGGTAGAGGAAGGGATACAAAAATAGAATTGGGATTGGGCCTAAGTCAAACTTTGCATAAAAAAGCACTTCATGGAACCTTTAAATGTGTGATGTAAATAATCTGTGTAATATTCTTGGCCATGTCTTGACACAAGAATGTCAAACACTTTTTTACTAACAACCTGAAATGCCCTTGAAACCACTTACCCAAAACCACTCATCCAACGGGCAACACCCTGACATTGAGGTGCAAAGTTTCACAGAGGTGTTTCTTTAGAAGATCTAAAAATGTGTCATTTTTGGTAGCATGTTCTTATTTCTTTTTTTATTTCTCTCCCTCTTTCATAG
Seq C2 exon
CTGTAAAGCACAGAGGAACCTGAACTCATTATTTGCGATTATTCTGGGACTGAACAGTCCTGCTGTCAGTCGACTTACTCAGACATGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074307:ENSDART00000114954:20
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:
PF0061714=RasGEF=FE(31.9=100)
A:
NA
C2:
PF0061714=RasGEF=FE(16.2=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:
CAAGAGTTGGTGTATTTTACTCTGA
R:
CTCCCATGTCTGAGTAAGTCGAC
Band lengths:
270-1587
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]