RnoINT0106580 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75411735-75412522:-
Coord C1 exon
chr7:75412432-75412522
Coord A exon
chr7:75411846-75412431
Coord C2 exon
chr7:75411735-75411845
Length
586 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGC
5' ss Score
6.08
3' ss Seq
GTTTTTACCTTTCAATACAGCAT
3' ss Score
6.58
Exon sequences
Seq C1 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
Seq A exon
GTAAGCCTCGTTTAGTTGTTTGGGAATTGGAGATGGGGATGGGTGGGTATGTGGGTGGATGATAACGTTTAACTTACCATGAGCTAGACTGTGGGTTCAATTTCCCAGTACTTCCTATTGTATAAGAGGCAAATTGCCCTGTTGCAGTGGTAAATTGCTTCTGGTAATTATGTTTGGTAGATTTGGCACATCCTTCGAGATGTTACTTAGACTGGTACTGACCTAGCAAGCATCCACCTCACCTTTGAGTGCTGAGAAGAGCGTGGACTGTCGTGCCTAGCTCTCAGTTAAAAAACTAAGTCAGTGGGTATTTGCTTCAGGTCTTCATTTGCCTTGGTAGTTATAACTTCAAAGTTTGCACTCTCCAGGAGGTAACCATTTTGGTCCTTACCCATTGCATAGCAAGCTGGGTTTAGGAGCACTTGGTGTTTCTTTTTCATTGTGTTTTTATCTCGAGTATTAAATTAAAATTCACTGTATACAAGGGTCTCTTCTAGCTTTTCATACAACCATTAGCCCTAGGAAAGCGTTGGCTCTCAGTCATTGAAATTCCCAGTTCATAATGAGTTTTTACCTTTCAATACAG
Seq C2 exon
CATTCCAGAATATGCCCGGTGCTATCCGCCCAGCTGCTCCTAGACCACCATTTAGTACGATGAGACCAGCTTCCTCACAGGTTCCACGAGTCATGTCAACACAGCGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.774 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCAGAACCGTGCTGCATAC
R:
ACGCTGTGTTGACATGACTCG
Band lengths:
198-784
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]