RnoINT0064012 @ rn6
Intron Retention
Gene
ENSRNOG00000057044 | Garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:RGD Symbol;Acc:1564019]
Coordinates
chr3:12041813-12043636:-
Coord C1 exon
chr3:12043498-12043636
Coord A exon
chr3:12042029-12043497
Coord C2 exon
chr3:12041813-12042028
Length
1469 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TTTTCCAAATTGTGTTTCAGGTG
3' ss Score
11.02
Exon sequences
Seq C1 exon
TCAGATATATACTTCACAGCAGCCACAACTGTGCATGAGGGCTCATCTGGAGGCAGCTCAAAGGGGGCCAGTGCACACACATCTCCTCAGACACCACCGGCCCGGGACACTCCACTGTTTCCTTCTTCCCTGGGGGAAG
Seq A exon
GTAAAATCTAGCTTGTCCTGTCGTCTTAATAGATGCTTTAGGGCCTCATGTCTTAGGCTTATTGTCAGAATTAGACATAATCACTGCTAAAGAAGTACTATTCAGGCCGGGCATAGCATCACACGCCTTTAATCCCAGCACTCAGAAGGCAGAGGCAGGTGGATCTCTGTGAGTTCCAGGACAGCCAGGGCTACACAGAAAAATACTGTCTTGGAAAACAAAAACAAAAAACAAAAATTCAAAGTAGGGATAGAAGTTATTGACATTGTCACTATCAAAAGCCAGTAAAAAAGGAAGACTTGCTTGGTTGCATGCCCAGCATTTGTGAGGTTGAGTGAGACAGAGAATTCCACATGCACTCAAGCAACAAACACAAAGAGAAGAAATCCCATCATGCAAGGCACTGCCTCAGTGTGGAAAAGGGAAATAGGCCAGAGGGCATCCAGCTGCAAGTTTCATGTGTTCCTCATGGGTGGGGACGGTGCTAGTGAGTTTCAAGCTAAATCTGCAGCCCTCAGGCCTCCGTGTGTCACTCTAGCTTTGCTCATTTTCCCCAGAGGCTTTTACCAGACTCCTGCAGGGCTGGGAACAGCAAGGGTTTCGTGTGCATTTTTGCTCCATCCATCTGTCCATCCATCCTCTTTATCACTTTTTGTTAGGATGAGTGTCCCAGGCACAGGCCCTTGCTCTCCTTGCCTCACCTATTTTTCTGTGCGAGCACAACTGACAACCAGTGTATTTTATCAAATTCACTCAGAAAGGGCTGGGGATTTAGCTCAGTGGTAGAGCACTTACCTAGGAAGTGCAAGGCCCTGGGTTCGGTCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAAAATTCACTCAGAAAAAGGGAAGCTTTGCAACAATCAGGATGAAAACTGAATAAAAAAGTAAGTTAATAGAAAAAAGAGAAAGGGGTTTCTTCATGCTAATGTTATTAAGGAACAAGAAATTATTTTCAAGCCAGCAAGATGGTCCTGCAGGTACAGGCACTTGTCATCAGGCCTGATGAACTGACTTGAATCCCTGTGTCAAATGAGAATAGATACCTGAGTCCTGTAACTCCTGACCTCCATAGAGGTACACGTGTGCACACGCACACGCGCACACACACACACACACACATTCAATAAATGTAATTTAAAACTTTGGGGGGAGCTTTGTTTGGTTTGGTGATTTTATTGTTGTTATTTATTTTTTGTTTTTTTTTTGTTTTATTTTTTAAGACAGGGTTTCTCTGTGTAGCCCCGGCTGTTCTGGGCTCTCTCTATAGACTAGGCTGGCCTCAAAGTCAGAGACCTACCTGCCTCTGCCTCCTGAGTGCTGGAGTTAAAGGCGTGCATCACAATTGCCCGGCTCGTACTTGAAAACTTGTAAAGGAAGAAGTTCTGTTGTAAATAACATGAGCCTAAAGTTCTGGTCTTTTCCAAATTGTGTTTCAG
Seq C2 exon
GTGAAATTCAGTCTAAAAATCTGTACAAGATTCCACTTAGAAACCTTGTGGGCAGAAGCATCGAGCGACCTCTGAAATCGCCCTTAGTCTCCAAGGTCATCACCCCGCCCACCTCCATCGGCCTTGGAGTCGCCGCCATTCCTGTCACACATTCCTTGTCCCTCTCCCGCATGGAAATTAAAGAGATAGCAAGCAGGACCCGCAGGGAGCTGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000057044:ENSRNOT00000082696:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.596 A=NA C2=0.356
Domain overlap (PFAM):
C1:
PF0078017=CNH=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGATATATACTTCACAGCAGCCAC
R:
GCGGGTCCTGCTTGCTATC
Band lengths:
342-1811
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]