DreINT0124564 @ danRer10
Intron Retention
Gene
ENSDARG00000079872 | rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:ZFIN;Acc:ZDB-GENE-070912-385]
Coordinates
chr9:2960266-2962261:-
Coord C1 exon
chr9:2962164-2962261
Coord A exon
chr9:2960352-2962163
Coord C2 exon
chr9:2960266-2960351
Length
1812 bp
Sequences
Splice sites
5' ss Seq
CAAGTACAG
5' ss Score
0.24
3' ss Seq
GATCTTGGACTGTCTTTCAGGTA
3' ss Score
9.01
Exon sequences
Seq C1 exon
GATGTGGAGGCAAACACTGTCCGTCTGAAGGAACATGAAGAGGACGTGCTGGTTTTGGAGAAAGCTAACAACAGGAGCTCCAGTTCTTCTCCTCTCAA
Seq A exon
GTACAGTCGTTTTCATCTGACAAGAAGTCGTTGTATTTGTAAACATTAGACTAACATTGACTTTGTTAGCGTTTGTTAGCATAGTTTAAGATCTTTGAATTCACATTTTATTAGTCACATACGGAGTCAAACAAAGCCCAAACTTTGAATGGGTTAGTCCACTCAAAAAGAAAATATGAATGAGTTACTCCACTGAGCCAGTGTGCAATGATTGGCCAAACACCTCAAGCATGTGTCAAAATGTAACGCAAGCAGGTCCTCTTTTAAACATTTTACAGGGGTAAGCTTTATTCTGTCTCCATGATTTGACAACAATATTCACTGAACTATAAGCTTTTAAGCAACTGAGTGCAGTTATGCTAATATATCAGATTTATTATGCTAAAATTTCAAAACAGGGGGGAGTTGGGTTTGGGCTGTGAGCCCGTGGTTTTCGTTTCTTCAGTTGTTATCTGAGAATAACATACCTTGGAATGTCACAACCAATCATTCATTCATTTTCTTTTCGGCTTAGTGCTTTTATAAATCAGGGGTTGCCACAGCGGAATGAACCGCCAACTTATCCAGGATACGTTTTACACGGCAGATGCCCTTATAGCTGCAACCCATCACTGGGAAACACCCATACAAATTCATCAGGGCTTAATTTGTGCCGAAACACTCCGGATCTGGCACCTCATTTTACCGATCCCGCTCCTCAACCGGCCTCCTCCCCCGTCAGCTGTGTACTTGAACTTTCTTCCGACTCCCCAACTCTTCACTTTCTTTCGCGACACCCCCGCCTCATTCACTATAGTGCACCTTTCCATCCTCGGGTAACATGTTGGATTCGTAATCCAGATCTGTTCCGGGACCTCGCAATTCACAAAGCCCGTGTTATTCGTTTCTGTAGTTGTTATCTGAGAATAACATACCTTATATGTCACAACCAATCATTCATTCATTTTCTTTTCGGTTTAGTCCCTTTAATAATCTGGGGTTGCCACAGCGGAATGAACCGCTAACTTATCCAGCATTTGTTTTATGTAGCAGATGCCCTTTCAGCTGCAACCCATCACTGGGAAACACCCATACAAACTCATCAGGGCTTATTTGTGCCGGAACACGCCAAAACCGGATTCACCACCTCATTTTACCGATCCCCCTCCTCAACCGGCCTCCTCCCCCATCAGCCGTTTACTTAAACTTTCTTCCGACTCCCCAACTCTTCACTTTCATTCGCGACACCCCCCCCCCCCCCCACTCACTATTGTTCACGACCCCCTGTGCCATCCACCGCACCACTCTACCCCAACACTTTTGTGCGCCGCACCTCTCTATCCTCAGGTAACATGCTGGATCGGTAACCCCGATCTGTTCCGGGACCTCACAATTCACAAATTAAGCACTGACACTCATTCACACTCATACACTGCGGACAATTTAGCTGACCCAATTCACCCGTACCACATGTCTTTGGACTGTGGGGGAAACCGGAGCACCCTAAGGAAACCTGCGCAAACACGGGGAGAACATGCAAACTCCACACAGAAATTCCAACTGACCCAGCTGAGGCTTGAACCAGCGAACTTCTTCCTGTGAGGCAAACGTGCTACCCTCTGCGCCACCGTGCAGCCCGATGTCACGACCAATCAGAATCAAGTATTCTGAGAGTAATAAAGCTTATTAATCCACACCTGTTCACCCAGTAAACAAAATAACCTCAACATAGCACCATATGGCCTCTTTAAGACTACTATAGTATAAGTGTAAACTGAGAATATCAACAACCTCAAACTCCAAATCAAAGTGTGATCTTGGACTGTCTTTCAG
Seq C2 exon
GTACACTGTGATGTCAGGAACTCCAGAGAAGATTCTGGAGCACCTTCTGGAGACCATGAAACTTGATTGCCAATTCTCAGAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079872:ENSDART00000144046:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.189 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.3=6.1)
A:
NA
C2:
PF0061815=RasGEF_N=PU(25.2=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTGGAGGCAAACACTGTCC
R:
TGACTCTGAGAATTGGCAATCAAGT
Band lengths:
182-1994
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]