DreINT0071462 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32777511-32778465:-
Coord C1 exon
chr5:32778361-32778465
Coord A exon
chr5:32777628-32778360
Coord C2 exon
chr5:32777511-32777627
Length
733 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CAATTTCAACTGTGCTACAGGGA
3' ss Score
5.04
Exon sequences
Seq C1 exon
ATTCACCAACCCTGCCTCCGGTGCAGGTATTTGACAAAACCTTGACCGTCAAACAAATGCACGTGCTTGAACCTCAGGACCTCCTCATTGCAAGAGCAGACAAAG
Seq A exon
GTAGGAAATGTGTTTGCTTTCATATTCATATGAGCAAATGAAAATGGTACAGATCTTGGGTGGGTAAAAGAAAGTGTGTACAATTGTCTGCCAAAGGAGAGAGAGAGAGAGAGAGCGAGAGAGAGCGTGAGAAAGAAACAATAAACCGGTGAAGGAAACTCTTGGTCTTTGCTCTAATGAGCATCTTTATCCAACTGGGAATAGCACAAAATAGTATCTCAAACACACACACTCAGGCACCATCTCTGGTTCACATTGTCTAGACTTAAAGCTCATTATAAGGAAAAGCACAGAGTAGAGATCCATGTAATTTAGTGTCTACCACCATCTTCTATTCTGATCATTACTGCAAGACACATGCACAGCAAACTCTGAGTTTTATTGGCAAGCACAGCTCTAGCAGAGGGAAAATAATGAATATGTTATCAACTCCGTCACCAAGCGACTTTCATTCACTATGACAGGCATTTGAAAACCAAACATGTTGCATTAGCTGAAATGTCATTCTGTTTGATGGGACGGCTCTCTCATTTGTTGCCAGGCTATTATCATACGGTAACGCTACTGAAAGCTTTTGTTTGCAGAATTAACTGAACAATTGAAATGGTCACACACTCCCCTTTGAATGCATTATTGAAACTGTACCAGGACTGCACAAGAGTACTTGAGGCTTAAAATTGCACGATTTGGTCTGATTTCAACTACTTTGTGTTCAATTTCAACTGTGCTACAG
Seq C2 exon
GGAAGGATGCTCGACTGTATGTTTACAGACTGAGCACACTCAAACAAGGTATAGAGGAGCGACAGCTCGTCCGCACCAAGTGTGACAGTCGAGAGAACAAGCTTGAGAAAACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:19
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=0.013
Domain overlap (PFAM):
C1:
PF0078017=CNH=FE(11.4=100)
A:
NA
C2:
PF0078017=CNH=FE(12.7=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:
ATTCACCAACCCTGCCTCCG
R:
CTTTGGTTTTCTCAAGCTTGTTCTCT
Band lengths:
222-955
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]