RnoINT0106602 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140986534-140987090:+
Coord C1 exon
chr5:140986534-140986673
Coord A exon
chr5:140986674-140986995
Coord C2 exon
chr5:140986996-140987090
Length
322 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GTTCTGTCCTGTGGTGATAGGTA
3' ss Score
6.55
Exon sequences
Seq C1 exon
GTTCGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCCGAGCTTGGAGCCAAGGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGAGAAGAGGTGGATGATGAGAATCTGAGGGAGCTATTCAGCCAGTTTG
Seq A exon
GTAAGTTGAGGCCTGGAGCCCGCATGCCCACTCTTGTACTGACCATACCAGGCTTAATCCGTTTTTCTTTCGGCAAGGACACTAACCTCAGGGGGTGGAGGGTGAACATAAAAGTCCAGGCCTTTTTCTCTTGGCTTCATCTCCGCTTTTTCCTTTGTAAGGTAATCCCAGAAGCTTGGTGGGGTTTTAGACCAGATTTGGTACCTCTTTCTGTCTCAGACCCATCTGGGCTCATCTGGAGATTTGTTCCAGCTGAGTTAGGAGCAAGAAGTCCTCGTGAGCTGTGGCAGACGTCACTAACTGTTCTGTCCTGTGGTGATAG
Seq C2 exon
GTAAGACCTTAAGTGTCAAGGTGATGAGAGACTGCAGTGGGAAGTCCAAAGGCTTCGGCTTCGTGAGCTATGAGAAACATGAGGATGCCAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:4
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCGTGGGCAGATTCAAGTCT
R:
TGGCATCCTCATGTTTCTCATAGC
Band lengths:
230-552
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]