DreINT0071469 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32767733-32769341:-
Coord C1 exon
chr5:32769223-32769341
Coord A exon
chr5:32767869-32769222
Coord C2 exon
chr5:32767733-32767868
Length
1354 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TCCTCTCTTTGTTTCTGTAGTCT
3' ss Score
8.71
Exon sequences
Seq C1 exon
TGTGTGCATTCCCATATATACTCGCATTCACCACAGACTCCATAGAGATCCGGCTAGTCGTTAATGGAAACCTAGTTTATACAGCTGTTGTTCCAGAATTGCAGTTGACTGCATCAAGA
Seq A exon
GTAAGTGTTCCAGCAATACCTTTTATGTGCCTTATACAGCTGCACTGGCTGTCAACAGGGACTTAGAAATTACATTTTTATTTATAAGTCTTAGACTATATGCTATAAAGTGTTTTAAAATGAACCATTTTCACATCTTACTGTATGTGATTTAGTTGCTGGATATATAACAATGGCTACGTTTCTATCCACCTATTTTTATGCACATTTTGGATATATGTGCATAATTGAGAAGAATAAACTTTTTATTCAATAAAAAAAAGATGCGCATAAACAATGATGGAAAGACTTTTACCAAACAAATTCCAGTATGCGCATTAAAAAAAGGTCATGTGATTTTGTTATAAGAGATCAAGTGTTGATAAAAATGTGTGTGAATGAAAAAAACAGCAGGCTGAGCACATTGTAGAACATCTGAAATGTTGTTTTGGTCATTCTAAAACCCCTTAACCATCTAAGTATTAGTGTTATATTATTAATGACCTCCAGAATCAAGAGCATCTGTGCTCCGTGTCTCACGCCTTCAAACACCACTGCACGTTCACTGCATGTCAGAATTGCCTTCTGAGGTGCAAGTTATTTATTAAATAAAGTGAAGATTGACACAAGCTTCTCCTACCGCAGCAAACTCCGTTTTTACTGTTGATATTTGGTGGCAGTTAATCAAGAAGTTTGATTTTTTTCTCTTTGACTCGTCTGATGTAAATGCTGCTTTATTTGCACATTTTTTACCTGCAAGAATCCAGTTTTATGCATAAAGTTAACTCACATTTTTGGATGCAAAAATAGCTCATACAGCATCATATATCATTTTTGTACTCATTTTAAAAAAATATATAATTCAAGTTTATTTGTATAGTGCTTTTCACAATAATTATTATTTCAAAGCAGTTTTGGAAAACGTGCTTGTCATTAAGAGTGTACAGATTGTTATATTTTTCAGGGAGGTTTCTTATGCTCACTAGGAGAGCATCCAGGTGATACAAACACAGTAAACATTAATATTGTTAAGTATTTGCTATTATTAATATTATTTAATGTTATTATCCTAATGTTAGCTTTGATGGTAAACCTTTTAATATTTATGTTGAAAAGACAGTGCTGCTTAATATATTTATAGAAAGTGTTATTTTTTAGAACTGAATAGAAAGTTTATTATTTTATTATTAAAACATTATTTATTATTAAAATAATTAGCAAAATAATCCTAAATTAACAGTATTAAATGTATTCATGATATTGTCATCCCTTTTATATGATTGATTTTTTTGTATGACATTTATACATTCTATTAAACAAAGCAGGATTCTCACTGATTTGATCTTGTCATCTCTTCCTCTCTTTGTTTCTGTAG
Seq C2 exon
TCTGATATCTATTTCATCTCCTCAGCGCCTATAAACTCTGCCTCTAACTGTAGCTCCAGAGACACTAGTTCCCAGAGTTCCCCTCAGACACCCACCGGCTATGAGATGCCTGTCTTCCCTTCACCGCTTGGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:25
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=0.533
Domain overlap (PFAM):
C1:
PF0078017=CNH=FE(12.7=100)
A:
NA
C2:
PF0078017=CNH=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGCATTCCCATATATACTCGC
R:
ATCTCCAAGCGGTGAAGGGAA
Band lengths:
254-1608
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]