DreINT0071466 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32769654-32771542:-
Coord C1 exon
chr5:32771384-32771542
Coord A exon
chr5:32769721-32771383
Coord C2 exon
chr5:32769654-32769720
Length
1663 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
GACTCTTCACTTTTCCCCAGGTC
3' ss Score
9.8
Exon sequences
Seq C1 exon
GAGATCTGCTTATGTGACTCTCCGGTGGTGATGGCACTGGTTGATGGCCCGACAGGAGAGAATGATCACATGATTTGTGTGGCCTACAGACATCAGTTTGACTTGATCAACGAGAGCACTGGAGACGCCTACAGACTACATCATGTAGATTCCAACCGG
Seq A exon
GTGAGAAACACATACGCCAGTGCAGATATACTTTACTATTCAAATGTTTTAAAGTCAGACATTTATGACTAATTTTATTTAGACAAAATTTTAAAAAGCAATTGACAATCTTGACAAATTGACAATTGCATTTATTTCAGAAATTATGCACTTGATTATTATCATTTTTTTAATTACAGCATTGATTTACAACATTACATATCTTATAAAGGCTGTTATGATAAACGTTTTATTCATCAACATTTTCAACAATGGTAAAGTGAAGAAATGTTTCTTGAGAAATGATTTGTGGGGATCATGTGACGCTAATAACTGGAGAAATGGTCATAATATTATTTTTACTTATTTTTATCTATTGAGAGCATAACAGACTTGCTAGCCTCAAACTGAAACAGCCTCGAACAGTAATGTGCACATTACTAATACATCCTTTCCTATATGTACAACATTTACTGTAAAAATAGGGAATTCCAGTAACACTTGTAATAAAGCAAAAAAATAATAAAATAAAATAAATGCCAGGGCGTCACTGTGGCACAATGGGTAGCATGATTGCCTCACAGCAAGAAGGTCACTGGTTCGAGCCTCGGCTGGGTCAGTTGGCGTGTCTGTGTGGAGTCTGCATGTTCTTCCTGTGTTCGCACAAGGAACCCCCACAAGTCCAAATACATGTGGTACAGGTGAATTGGTCAAGCTAAATTGTCCGTTGTGTGTTTGTGTCAATAAGTATGTATGGATGTTTCCCAGTGATGGGTTGCAGCTGTAAGGGCACCCGCCGAGTAAAACATATGCTGGATAAGCTGATTAATAAAGGGACTAAAGGCTGCTTTATACTTCTGCGTCAAGCGCACGCATATGATCCAGCGCTCATTGTGGACGCCACCGATGCTGACACGCAAAAAATGTAACTAAACGTTGCAACAACGCGTAGCGCAAGCTCTATGATTGTTCAGCTAGATAGTGCTGACGAGTGTGGGCGGAGGTGAGAGCCACGCGAGCCCTATGGAGCGAGTGTTTACAAGTGTTGAGTCTCATGAATGAGCTCTAAATAGAAAATGTTGTTTTGTGTTTACCTTATGAATAAAGTTGTTGCACGTCTGCTGATTCCCACCTCAAAATGAGCAAGTTTGAGCCACTTGTACATTAAGGTAGCGATCCGAAAAACAAAACACCAGCGAAGAAACTCGACATAGAGGAACATAAAAACCTCACTGCCAGCTAGCGTTTCAGAAATGCTATTGCAGAGCAACAGAAACAGTGCGCAGAAGTATGAATGCACGACAATGCGCATTGCATGCGCCGTGGGTCACGCCAATCACTCGACGCAGAAGTGTAAACTAGGCTTAAGCCGAAAAGTAAATTAATGAATGAATGAAAATAAATGCCACTGCGTTTTGGCTTAAAAGACTTCTTCCGCGCACAAAAACATATCACCATTTGATTTATTTTATTTAAAAAATGTTTTCCTTTTACAACAAGTGTTGTTGGAGTTCCCTATTTTTACTATATTTTGTCTCTACTGCATTTTGTCCATGCACATTATATGGTGGTTGAGTGCTCAAATTAATCCCTTACTAAATTTTTTTTTTGTATTACCACTGTATTGTATTTGCTCATTTACACGAAAAACTATTATTGACATGGACTCTTCACTTTTCCCCAG
Seq C2 exon
GTCAACTTTGTTGCTGCCATAGACGTTTATGAAGATGGAGAGGCTGGACTTCTTCTTTGCTATAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:22
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:
PF0078017=CNH=FE(16.9=100)
A:
NA
C2:
PF0078017=CNH=FE(7.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCTTATGTGACTCTCCGGT
R:
TGTTATAGCAAAGAAGAAGTCCAGCC
Band lengths:
222-1885
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]