RnoINT0144543 @ rn6
Intron Retention
Gene
ENSRNOG00000027447 | Stam2
Description
signal transducing adaptor molecule 2 [Source:RGD Symbol;Acc:1311497]
Coordinates
chr3:38249910-38251741:-
Coord C1 exon
chr3:38251595-38251741
Coord A exon
chr3:38249980-38251594
Coord C2 exon
chr3:38249910-38249979
Length
1615 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATTTACTCACACGCTTACAGACT
3' ss Score
5.42
Exon sequences
Seq C1 exon
GCTCATCCTAAAGTATGTGAAAAACTGAAATCTCTAATGGTAGAATGGTCAGAAGAATTCCAGAAGGACCCCCAATTTAGTCTGATATCTGCAACTATTAAGGCTATGAAAGAAGAAGGAGTTACTTTTCCTTCAGCAGGTTCCCAG
Seq A exon
GTGAGAGATGTGTTCAGACCATGTCCCCTACTGTCTGAAGGCACTTATGCAAAAGCTAGCAAGGCATGTGGGTTTTATTTAAATGTGCTTGTGTGTGTGGGTGTGCATTTGTGCACAAGCATGTGTGTGTGTGTGTGTGTACACATGTGTTCTTGTGCACACTTGTGTCAAAGCAAGAGACTCGTGGTCAGAGACAACTTGGGGAAGTTGGTTCTCTCCTACTGTGGGTCCTGAGGATGCAACTCAGTCATGCGGCTTGGCAGCAGGTACGCTCGTGCTGAGCAGAGATCAGCAAGGCTGAGTTCTTAGCGGGAATGTCTTACCATTTCCCATCTGCATCCCCCGAGCGTCTAACATAGTACATAGGTTCTGTTTAGTAGAGACATCTATTGTTTGGTATTTTTCTTCTAAATACCAGAAACTTAGGAATCAAACCAGATATAAATAGTGTATTGAATGTCACTCTAAAGTCTGGACTCACGTGAAAAGTGTAGGATGTTCCAGTCAGCCTTATGTTTAAGCAGTTAATGATCAGGGGCTGGTGAGACAGCTCTGTGGTAAAAGTACTTGCCATCCAAGTCTGATAAAACCTGAGTTCAGTTCTAGGAACCCCTGAAAAGTGGAAGACAAGAACCGGCTCAGAAACTCTTCTGATCTCATTCACACTGTTAGGTGTCCCCCTACTTCCTCTGATATAAGTTAACACATTTTAGAAATTATGCTAGATTTGAAAGATGGTCATACATCTGAAACACAGTACTAATTTAGATTGCTAGTGATGAGGACCGATGGATGAAGATGCTGTCTGTCTTAGCACCAAGGAGCAAAAAGGACTGCAGATTGCAGTGGTGAGGACACGGAGGAAGCACGTTGTGTTCACATTAGGTAGAGTGGGATGAGGAGATGCTGGGAAAGGGCCGGTGTGCACAGAGCTCTGGAGTTGAGAATTGCCTGAGGAAAGTGAATATGCGGGAGGTAAGAAGCCAGTGAGCTGTTAGAAGTGTAAGGCCTGAGGCTCACGTGGAGACGTGAAGCAGTGGGACAGTGGGAAGGGAAGAAGGGCACAGTGGTCTACTAAGTAAGGAAGAGCAGCCCATCTGCCCTTCTCAGAAATGGGTGTTAAAGAGTTATTGGTGGCTCAGAGTCCTGGACACCTGTCGTAGGTCCGTCCGTCAGACGGAAGAGGATCATGTGAGTCAGAGGCTGCCTCTCCCGCTGTAGTAAGCAGTCGATGACCAAGGTGTACCAGGGACGTCTCTTCTCTCTGTCAGAGCTCTGAGCCAGTAGCTTCTGAGCGTCTCCTGCATAAAGACCTTCAGCAGTCGAGAACCAGGCTCTGTTCATTCTGTAAAAATTTCAATACTTTCTTTCTGCCAAGTTCTCTGTCAGGTTCTTAGATTTATTAAAGTGTTAGTCAGTGTGTGCCTTTCGTGTGTTTGTTTCCTTGAAAACTGATGGTTAGTGTTAGTATTTCAGAACAGCTACTTAAATGATCATGAAGCCCTCGCTTTTAAATGGAGTGGTTGCCGGTGTTTTTAAGTTAGCATCTACATGTAATTATGCAGTGTGCTTCCTTTGAAAGAATAGCTGTGCTCATTTACTCACACGCTTACAG
Seq C2 exon
ACTGTCTCGGCTGCTGCCAAAAACGGGGCATCACTGAACAAAAACAAAGAAGACGAGGACATAGCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000027447:ENSRNOT00000037857:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.458
Domain overlap (PFAM):
C1:
PF0079014=VHS=PD(28.5=79.6)
A:
NA
C2:
PF0280915=UIM=PU(50.0=37.5)
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:
GCTCATCCTAAAGTATGTGAAAAACT
R:
TAGCTATGTCCTCGTCTTCTTTGT
Band lengths:
214-1829
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]