HsaINT0119412 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101721361-101721959:-
Coord C1 exon
chr8:101721687-101721959
Coord A exon
chr8:101721452-101721686
Coord C2 exon
chr8:101721361-101721451
Length
235 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TGTGCTTTTTTTCCCTGCAGACT
3' ss Score
12.79
Exon sequences
Seq C1 exon
GTTATGATGGAGGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCACTAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTTCCCAACCCTGTAATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTAGGTTTTAGAAGGCAACCAGAACCATGAAGGTTTTCGTATTTGGTCATTTCTAGTGTTTTTTGTGCCCCTCGCCCCGCAAATGTGAAACATTAAGAAAGGGGAATTATGATTGAGTAGGAAAAAATGCTTGAGTGTGAAGTCCTGGTAAATGTTTTGAAAAAGTACATATAATTTATTGCATTATTTGCTTTTTTCTTCAACTGATAAACTCATGTGCTTTTTTTCCCTGCAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.235 A=NA C2=0.657
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTATGATGGAGGGTGGTCGC
R:
GTATGCAGCACGGTTCTGAGT
Band lengths:
294-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)