HsaINT0119405 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101715144-101716618:-
Coord C1 exon
chr8:101716525-101716618
Coord A exon
chr8:101715588-101716524
Coord C2 exon
chr8:101715144-101715587
Length
937 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGC
5' ss Score
5.89
3' ss Seq
TGTTTTTTTAACATTTACAGATT
3' ss Score
8.78
Exon sequences
Seq C1 exon
GTTGATGAAGCTGTAGCTGTACTACAAGCCCACCAAGCTAAAGAGGCTGCCCAGAAAGCAGTTAACAGTGCCACCGGTGTTCCAACTGTTTAAA
Seq A exon
GTGAGCTTTTCCCTCTGGTTTGTTGTTTTAAGCTTGTTTTCTTCATCTTTTATAAAGTTTGTTGAGCATATTTTGAAATGTACATAGCAAAAGATCATTTTACAGTTCATTTAAATGTATTGCTAATTTTTCAAGGAAAAGTGGAACTAACTATAGAGGAATTAAAGGAATTTTACCCGTTAACTGTTGGATTTTTAAAATCCCAGGACTTTCAGGTGGTGTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTTTCGTTCTGTCGCCCAACCTGGAGTGCATTGACGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCCTGCCTCGGCCTCCCGAGCAGCTGGGATTAACAGGCCCATGCCTGCCACCGTGCCCAGCTAATTTTTGTATTTTTACTAGACTTGGGGTTTTGCCATGTTGGCCAGGCTGGTCTGGAACTTCTGACCTCAAGTGATCCGCCCACCTCGGCCTCCCAAAGTCTTGAAATTACAGGCGTGAGCCACTGCGCCCTGCCAGATTTTGTATAGTAATATATATATAAAATGACCTGTCACAGGTTGGCTTTCATAGTTTTACCTTTCCTTTTTGGGTGGTGCCCTTGGGTCTCTACTACTGTCTTTCATCACTCCCAAGAAATTGAGTAGTGCAGCCAGGATCAGGACCAGGGATTGGCAAATGTTTTTTGTAAAGGGCCAGATAGGAAATATTTTGGGCTTTGAGGACTGTGTTATCTCTGAAATGATCTTGTTCCAGTGTTACCATGTCAAGACAACCATAGATAGTATGTATACAAATGAACAGGTATGGCTGTGTTCCAGTAAAACTATGGATAAAAACAACCACATTGCATTTGGCTAAGGGCTTTAATTTGCTACTGACAAGTGATAGTCCTGGTCTTAATTTGTTTTTTTAACATTTACAG
Seq C2 exon
ATTGATCAGGGACCATGAAAAGAAACTTGTGCTTCACCGAAGAAAAATATCTAAACATCGAAAAACTTAAATATTATGGAAAAAAAACATTGCAAAATATAAAATAAATAAAAAAAGGAAAGGAAACTTTGAACCTTATGTACCGAGCAAATGCCAGGTCTAGCAAACATAATGCTAGTCCTAGATTACTTATTGATTTAAAAACAAAAAAACACAAAAAAATAGTAAAATATAAAAACAAATTAATGTTTTATAGACCCTGGGAAAAAGAATTTTCAGCAAAGTACAAAAATTTAAAGCATTCCTTTCTTTAATTTTGTAATTCTTTACTGTGGAATAGCTCAGAATGTCAGTTCTGTTTTAAGTAACAGAATTGATAACTGAGCAAGGAAACGTAATTTGGATTATAAAATTCTTGCTTTAATAAAAATTCCTTAAACAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:14
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(11.1=22.6),PF085466=ApbA_C=PD(37.7=83.9)
A:
NA
C2:
NA
Main Skipping Isoform:
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:
CCCACCAAGCTAAAGAGGCTG
R:
GCTGAAAATTCTTTTTCCCAGGGT
Band lengths:
346-1283
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)