Special

RnoINT0145192 @ rn6

Intron Retention

Gene
Description
serine/threonine kinase-like domain containing 1 [Source:RGD Symbol;Acc:1307355]
Coordinates
chr3:5493187-5493653:+
Coord C1 exon
chr3:5493187-5493305
Coord A exon
chr3:5493306-5493489
Coord C2 exon
chr3:5493490-5493653
Length
184 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGC
5' ss Score
5.2
3' ss Seq
GATGCCCTCTTTCCTTGAAGGAC
3' ss Score
9.1
Exon sequences
Seq C1 exon
ACCCCTGCCAGAAGTCCTGGATGGCTCCTGAAACTCTCAAATTCTCCTTCTCCATCAAATCCGACATCTGGTCCCTGGGCTGCATCATTTTAGACATGGCCACGTGCTCCTTCCTGAAT
Seq A exon
GTGAGCTCCCTATGGGGAGGCTGCCTACTTTCATCCTACCCTCTTTCTTTCTCTGGCCCATGGAGGCTCACTATGCTCACTTTCCTCAGGCCCCTGCCTCAGCTCTTGCTGGGCCTGACGAGAGAGCACTGATAGATACCTTCCTGGCTGAGAAAAGCCCAGGTGATGCCCTCTTTCCTTGAAG
Seq C2 exon
GACGCAGAAGCCATGCACCTGCGGAAGTCCATTCGCCACCATCCAGGCAGCCTGAAGCCCATCCTGAAAACCATGGAGGAGAAGGAAATCCCTGGTACAGATGTCTACTATTTGCTTCTGCCCTTTATGCTGCATATCAACCCCTCTGATCGACTATCAATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000027911:ENSRNOT00000031316:8
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=0.018
Domain overlap (PFAM):

C1:
PF0006920=Pkinase=FE(14.4=100)
A:
NA
C2:
PF0006920=Pkinase=FE(19.9=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTCCTGGATGGCTCCTGAA
R:
TGCAGCATAAAGGGCAGAAGC
Band lengths:
242-426
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]