RnoINT0106592 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160430332-160431529:+
Coord C1 exon
chr3:160430332-160430580
Coord A exon
chr3:160430581-160431438
Coord C2 exon
chr3:160431439-160431529
Length
858 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
CGGATCCTCTTCCTCCACAGTCT
3' ss Score
9.08
Exon sequences
Seq C1 exon
GTGATGACAGAAAGTAGCCACAGCAAGGGCTTTGGCTTTGTGTGCTTTTCCTCTCCAGAAGAGGCAACGAAGGCTGTGACAGAGATGAACGGGCGCATCGTGGGTACGAAACCACTGTATGTGGCCCTGGCACAGCGCAAGGAGGAGCGGAAGGCCATCTTGACCAACCAGTATAGGAGACGCCTCTCTCGCTCTGTCTTGAGCTCCTTCCAGCAGCCTACCAGCTACCTGCTCCCTGCTGTACACCAG
Seq A exon
GTGACAGGATGTCTCCAGCTCCGGCTGAGGGAACAGAACGTCACAGACAGAGGTTCTGTTGAAATGACCTTGGACAAGCTGCTCCAATCCCTTAAAGCCTCATTTGATCTGTCTTTAGAGGGGCCTACATGCTTTCTTGTCTTCTAATCTGTGGGAGATTCCTGAATGTTGTCTGGAAGGGACTCCGTGGTTAAATGAGTTTTGGAGATCTTGAATTAATCAAAGCTTGAATTTCTTTATTGTATCCATTATCTCCCCCAGTTATGTTGGAATCAACCTATCTATTTATTTATTTAATGTGAATATACTGTCACTCTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTATGTTGGAATCTATTGGGCTTCTTAAACAGCCACAGCACCTGTAGCGTTTTTCCCAACACAGCTGCCATGGCTGTTGCATTCTGAGGAGATGGCTAGGGAAGTGACCTCATAGAACTCAGAGCAGTAAAGAGGAATTTGTGATTGAAGACCCATTGCTAACATTCTTCAGTGATTGCTTGAGCTGGAACAAACTGGAGTGGCATATTTTATCTAGGTCACTGGGTCAGTGTAAGGAGCAATGGTTGACATAAATCCGAGGTCTTGCTCTGAGGGGTTCAGGGATAAAGGGAGATGAAGTGGGAGGGTGGATCCTCCACGGAGCCCTGAGCTGCTTCCTATGGGGGATAGTGTTGTGTCCTTGAGAAGAGTTGGAGCTCCTCACCTCGGATCCTCTTCCTCCACAG
Seq C2 exon
TCTACAACCCAGACTATGTACTATAGTTCTGCCTCCATAGCCCCAATGCAACCTGACCCCAGGTGGACAGCCCAGCCTCATGGACCTTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=0.581
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=47.0)
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:
ACAGAAAGTAGCCACAGCAAGG
R:
ATGAAGGTCCATGAGGCTGGG
Band lengths:
334-1192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]