RnoINT0106588 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160419417-160419829:+
Coord C1 exon
chr3:160419417-160419556
Coord A exon
chr3:160419557-160419734
Coord C2 exon
chr3:160419735-160419829
Length
178 bp
Sequences
Splice sites
5' ss Seq
TTGGTGGGC
5' ss Score
3.03
3' ss Seq
GCCAGTTTGGTCCTTCCTAGGAA
3' ss Score
6.55
Exon sequences
Seq C1 exon
TTTCGTAGGTCACTTCAAGTCTCGCCAGAAGCGGGAGGCAGAGCTGGGGGCTCGGGCCCTAGGATTCACCAACATCTATGTGAAGAACCTGCGCGTGGACATGGATGAGCAGGGCCTCCAGGACCTCTTCTCCCAGTTTG
Seq A exon
GTGGGCATGCTCCCCAAAGGAGAAGGGGAAACACTATCGCTCTTCTTCCATGCCCAGGTCCGGTGGGAGGAGGGCTCCCCACTCCCGTCCCCGGGATTCCGGGGGACTTCTATAAGAAGGAAGGGACCTTGCTGGCCCTTCCTCTGACTCCCTGCTAAGCCAGTTTGGTCCTTCCTAG
Seq C2 exon
GAAAGACGCAGAGTGTGAAGGTGATGAGAGACAGCAATGGGCAGTCCCGGGGCTTCGGCTTCATCAACTTTGAGAAGCATGAGGAAGCCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:4
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=0.031
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCGTAGGTCACTTCAAGTCTCG
R:
CTTCTGGGCTTCCTCATGCTT
Band lengths:
234-412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]