RnoINT0083137 @ rn6
Intron Retention
Gene
ENSRNOG00000054488 | LOC500584
Description
similar to casein kinase 1, gamma 3 isoform 2 [Source:RGD Symbol;Acc:1598209]
Coordinates
chr5:164348017-164348713:-
Coord C1 exon
chr5:164348469-164348713
Coord A exon
chr5:164348125-164348468
Coord C2 exon
chr5:164348017-164348124
Length
344 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTG
5' ss Score
8.35
3' ss Seq
CTAAGTTGTATTAATTTCAGCTT
3' ss Score
4.15
Exon sequences
Seq C1 exon
AAACAGGGCCATATTGAAAGGAAAAGAAAGTTGGAAATTGAAGTTTTATGTCATGAACTATTGAAAGCCTTCGTAGATGCTGATGAAAATGGCTATACCTAAATCTGATGACAACTTATTCTTTTGTAGAACCCATGATATTTGGCAGATAGAATCTTTGTACTCCAAGACTATAGGATACATATGGAAAATAGATGTACTGTATCTGCTTGGTAAAAAGAAGTCGAACTTCACCAACGTGTCAG
Seq A exon
GTATTGTGTTTGATTGTAATGGCTAATGAAACACCATTCAAATCTAGGTCATCAATCAGGGTAGCCATTAGCCATTCATCCTTGACTCTAGACCCAGGGAGATAAGTTCTCAGTAATAACCCTGAGTAGTCGTGTTTTACAGCAGGTGTTCATGTACTCTATGTTTGTGCCTGGTGCCTGCTGATGTTACAATAGACCTCAGATTATACTCATATTCCTACACAGTAATTTGTGACTCCATGCACACGTTTCTGTAGAAATGTTGACAAGATTCTTCATATTTTGTTTTTAATATCCTTTTATGTGGGTAAGCATTGTCCGTAACTAAGTTGTATTAATTTCAG
Seq C2 exon
CTTTTAGTTTTCAAACCTGGTTGTGAAATTTCAAGAAAACTTCCAATATTTGAATCTGTGAGAAGAACAGCAAAAAGAATGAGTGTGGCTCTGGGAAACACTCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054488:ENSRNOT00000087044:1
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGGCCATATTGAAAGGAA
R:
GTGTTTCCCAGAGCCACACTC
Band lengths:
344-688
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]