DreINT0074569 @ danRer10
Intron Retention
Gene
ENSDARG00000017311 | gpsm2
Description
G-protein signaling modulator 2 [Source:ZFIN;Acc:ZDB-GENE-040426-1169]
Coordinates
chr2:45649188-45649833:-
Coord C1 exon
chr2:45649612-45649833
Coord A exon
chr2:45649324-45649611
Coord C2 exon
chr2:45649188-45649323
Length
288 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGC
5' ss Score
7.53
3' ss Seq
TATATAAATCATATCCTTAGGAC
3' ss Score
6.75
Exon sequences
Seq C1 exon
GATGGAGGCGTCCTGTTTGGATCTGGCTCTGGAGGCAGAGCGTCTGTGTAAGGTGGGAGATTACAGCGCCGGTGTTTCGTACTTCGAGGCTGCCATACAGGTTGGCACAGAAGACCTACAGGTTCTAAGCGCCGTCTACAGTCAGCTGGGGAATGCCTACTTCCACCTGCACGACTACAGCAAAGCTCTGGAGTTCCACCACCATGATCTTACACTCACTAG
Seq A exon
GTATGCACGTGCTAACATTTTTATTTTTTTGCTTTGGTAACAATGTACTCAAAGTAACATTATACACATCTAAAGTGGTACAAGAGGTTTTTACTGTACATTATGCTGTTGTGTTCAGTGTTGCATTAATCAAGTAATCCTCAGGAACAATTGTTACAATATTTGATGTATTTTATTATATAAATAAGATACTTATTTTACACTCAAATAATTCCAGCAATGTATAACTATTAGCTAGCTTCAGTTTGCTAATATTTTATAACATTTGTATATAAATCATATCCTTAG
Seq C2 exon
GACCACTGGTGATCGGCTTGGTGAGGCCAAAGCCAGCGGAAACCTGGGGAACACATTAAAGGTTTTGGGACGCTTTGATGAAGCGATTGTCTGCTGCCAGAGACATTTAGATATTGCCAGGGAACTGGGTGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017311:ENSDART00000024034:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.001
Domain overlap (PFAM):
C1:
PF0206410=MAS20=PD(76.9=80.0),PF134241=TPR_12=PU(62.5=46.7)
A:
NA
C2:
PF134241=TPR_12=PU(62.7=80.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGCGTCTGTGTAAGGTGG
R:
TGTCTCTGGCAGCAGACAATC
Band lengths:
292-580
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]