RnoINT0145176 @ rn6
Intron Retention
Gene
ENSRNOG00000027911 | Stkld1
Description
serine/threonine kinase-like domain containing 1 [Source:RGD Symbol;Acc:1307355]
Coordinates
chr3:5481522-5483078:+
Coord C1 exon
chr3:5481522-5481812
Coord A exon
chr3:5481813-5482991
Coord C2 exon
chr3:5482992-5483078
Length
1179 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
TCTCTCTTCTCTGAGGGTAGATT
3' ss Score
3.21
Exon sequences
Seq C1 exon
GCCCAACACACCGGGCCCCGCCCTTCGTCCCGTACGCGGCGACCTATTCTCTGGCTTCTTTAAGGGGCATAGAGCAAGTACGCCATGTGCGTGCCAAAGTGCTAAGCAGACACGCCCCGGGTTGAGGGTTATGGAAGTCAGGTGGAGGGACTGAGGAGGTGGGGTGGGCACACGGAGCAGTCACTACCGAGCATGCTCAATCGAGGGTTCGACTACCGGCCTGGCTCGAGGGCTTAGCCCCGCAGAGGGACAGTGAGGCTGTCTTGTCGAGATACCATGGAAAAGTATCAG
Seq A exon
GTGCTGAGATGCCCCCAACCAAGGCCCAGAGTCCGTAGGTAGCAGGACAAGTCCGAGGTTCACACAGCCAGGCCCATCTTCCATCACAGGTTGACCCCATAATCCCCGCAAGTTTCCTCCTCTGAGTCCTCCTTCGAGTCCTCCCAGGGCCTCAGTTTCCCTCTAAAATGATGACTAATCGCCCATTCTGACCTCTGGTGCACGTGCCCTTCCCTCCATGTATGGGGGACTTTAAAGGGAGAACATAGAACCAAAAACCTGAGTGGATTTTTTTAAATTGCTTTTTTCCTGACACATCAGATTTATTAAATGTCAGAGTCAGTTTATAAAAGCTTCGCTTTCGCGCATTCACTTCTCTTCTCTTTTCTAGCATTCTCTGAGAGAAGGTTTTAGATGCGTTAGCCAAGCAAATGCACTTGTGATGGCAGAAATGTTTAAAGAAAAAAAAAAAATCCACTGCTCACTGACCCGGGGTTGGGCTCCAAAGACTCCCTGTATCCTCTGCATTCTATCCTTCCTGAACTGCCTACATATCTTGTCGCTTTCCCCACACTGACAGCAGCCTCAGTCCTCAGGCTCAGTCACCCTCTACCCGACAGCACTGATCTTATAAGATCTAGCTTGCAGACTAGTTCTGAAGGTGTGGCTTCAAACATGAGCTCTGGCTCAGACCCCAGAGTGCCATAGCCACAGGCAAGGCAGGACCTTGCTCCCTAGGCCTCAGTATCTCTCAAGTAAATTGTAGGTAGCACCAGTGCAGGTCACAGAGGATGACTGGGAAGGAAGCGCATCCTTCAGTGCTGAGCCCTAGAGGAAAGCGATGACTGCACCAGTTATATGCGTTAAGGGCCTTATTTGGATGTTGATGTTGGAGAAGGGTACTGGATGGGGGTGTCACTGGGGTTAAGAGCCACTGAAGCCCACTGTTCCCCAGGGGAACTTTCCCCTTGCAGGCCTGGGGGAGGTCCTGAGGCTGTAAAATAAGGGCTCCAGAATGGGTTTCAAGGGAAATTGTATTGGCTCCACCCTAGAGGGCTTCTCAGTCCATCACCGAAGACCATTTCCTCTACAGCAAAATTGAGAGAAGATGCTGGCTTGGGGCCCAGTGTGGACTCATCACGTGTGGGAAATCCAGAATAATGTGCACTTTCTCAAACTCTCTCTCTTCTCTGAGGGTAG
Seq C2 exon
ATTTTGCAAAAGCTGAGTCCTGGGGCCCTAGGGGTGAACCTGGTGGTGGAGGAACTGGAAACTGAAACCAAGTACTTGATAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000027911:ENSRNOT00000031316:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(0.4=20.0)
A:
NA
C2:
PF0006920=Pkinase=FE(10.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGCCCTTCGTCCCGTAC
R:
GGTTTCAGTTTCCAGTTCCTCCA
Band lengths:
343-1522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]