RnoINT0106593 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160431439-160432365:+
Coord C1 exon
chr3:160431439-160431529
Coord A exon
chr3:160431530-160432248
Coord C2 exon
chr3:160432249-160432365
Length
719 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
GTTTTTCTCTGTGCTGTAAGCTA
3' ss Score
3.47
Exon sequences
Seq C1 exon
TCTACAACCCAGACTATGTACTATAGTTCTGCCTCCATAGCCCCAATGCAACCTGACCCCAGGTGGACAGCCCAGCCTCATGGACCTTCAT
Seq A exon
GTAAGTGACCCAGCCCTTCCCACCTTCAGCCTAGCCTGTAGATGTGAGCCTCAGGAGAAGAGGCAGTGTACAACTATGGAATCAAGCCTGGCTTTGCATTTCTCAGAATTGTTTACCCCTGCCTCCTCTGAGCCTCAGTTTCCTCTCCTCAACTTGGGACTAAATGAAATGTTCATGAGGTGGCAAGCACTATGGCAACCCTGGCAAAGACACATTGTGTGGCCGGACACATAGTCTGGTTTGGGGCTGAAAAATCTTGCGAAGCAGGGAATTAAAAAGGAAACCCTTTTTGGCTAAATTGTTAACGAATGGCCTTTCTGAGCACCCAGCTTAGATGCAGTTCTCTTGGGACTCAAGTGAATGGTCAGGGCACTTGAGAAATTGAGGATCTGGGGAAAAAGAGCTGGTTTTGTCATTGCAGATCTCTGTACACGCTCCATAGAGTTCTTGGTATTGGTAAATTCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTCCTCTCTCTCTCTTTGTCTCTCTCTCTCTCTGTCTGTCTGTCTGTCTCTCTGTCTCTGTCTCTCTGTCTCTGTCTCTCTTTGTTTGCCCGTCTGTCTCTGCTGTGAATCTAGCTCCTCTCCAGCTCCGGGAACTTAGGGCACAGCATGGTACTTTGATTATCACCCAAAACCTCTCTCTGTTTTTCTCTGTGCTGTAAG
Seq C2 exon
CTACCTGCCCTCCAGCTGCCTCGGTGGTCCAGCCTCTAAGCACGGCACCGCACCCCTGTATCCACCTCAGCAGTGCCAGCCAGGCCTCCAGCCAGGTGCCTCACACGCAGAGAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.581 A=NA C2=0.700
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
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTATAGTTCTGCCTCCATAGCCC
R:
CTACTCTCTGCGTGTGAGGCA
Band lengths:
190-909
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]