HsaINT0119408 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101725315-101727829:-
Coord C1 exon
chr8:101727690-101727829
Coord A exon
chr8:101725410-101727689
Coord C2 exon
chr8:101725315-101725409
Length
2280 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
TATGTAAAAAAATTTTTTAGGGC
3' ss Score
6.18
Exon sequences
Seq C1 exon
ATTTGTTGGACGATTTAAGTCTCGTAAAGAACGAGAAGCTGAACTTGGAGCTAGGGCAAAAGAATTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGTTTG
Seq A exon
GTAATGTGTCTTAATTAAATTTTTACACACAAAGCTCTGAATTAGTGCTCAGTGTTAATTTTAGCTATTACTTTATACTAAAAAAGTCAATAAAATTAGACTTACATGGTACTTTAAAATATTTGTGGTTATTTGAATTAAGCTGCTGGCCATCTATTACACTACAAAGTAGTATAATGCAAATAAATAGAATTCTATCCAGGTTAAAGGTTAATAGCATTAGATTAGCACAGTAAGGTATGACTAAGTAATTAGAACAGATTTTAAAATATTTTACTACATTAAGAGGCTGGAGATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAATTAGAGATCCCATGTCATCAGAAGCATATATTTGACACAGCCAGCCTACAGTGGAATGCAGTCTCATAGAACAATAAAGCTGGTCAGTCTAAGTAACATCATGTTTGAGCAGTTTAAAACAATGACTTTCAGCGATGAAACCAAAAATTCAGATTTTCCAGTGATTCAAAGTACTTATTTCCTGCATTTAAAAATAACTTCATAAAACTTGAAATTGATGAAGCACAAACCAGCCTTAGTTTAGGTAGGGGTATAACAGATAAAATAACTTTTAAGTGTTCATGTGCAGATGATTTGCTTGACCCCACCCTTTGCATTTTGTGTTGAACTTAGAGGTGTCTTGCTTTTTTTAATATGTCAAATAATAAAGAATTAGGAAATCTAATACTTTTTTTTTTGACTCTTGCTCTGTCACCCGGGCTGGAGTGCAGTCACGTGATCTCGGCTCATTGTAGCCTCCGCCTCCCGGGTTCAAGCAGTTCTCCTATCTCTACCTTGAGTAGCTGGGATTACAGGTGTGCGCCACCATGCCCAGCTAATTTTTGTATTTTTATTAGAGACGGGGTTTCACCGTGATGGCCAGGCTGGTCTCCAACTCCTGACCTCAAGTGATCCAGCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCTGGCCAGGAAATCTAATATCTTACTGCCATGCTAGCATGTCACATCAAGCCCTCCACTAGAGCAAAAAAGTACCATTTTGCACAAAGATAGATGATATAAAACATAGAAAGTGACATCATGTTTACATCTCAACCCCCAAATTTAGCTACTGCCTTTTATATATTTCAACTGTCATGCTTCTTAATGTCTTATAATTAGAAGCTGTTTGTAAAAGTTGATGTTAACTACCTACCGTATGAGTAATGCTGCATAAGTTGACCACAAATATGTGAATATGTCATATTTTCTTGACTTTGGCCTCAGGAGAGAGGCACATTCAGAAGAAAATCTGCCTTGGCCCATACATCTTCTAAATTTCTGTAATCAAATGTGATTTTTAACCTTTTCTGCCCCACTTGCCTGAGATACCACCCGCCTCAGTTACCTGTCTCTCCTACTTTAGAGGGAGTTAGGGGAAAACATGTCTTCAGAAATAAATGCTTCCTCTTCCAGGTAGTTCACCTGTGTCTTTAAAAAGAATTTTTTTTCCCTGTCTTTCAAATTCCTGTATTACCTATGTCTTACCAAAGAGTCCAACTATGTATTCCTTCCACTCCTGTTGAAAGTCGGGTAGGCCAAGGCTTAATAAATACTTGTTTCTTAATTGATACAAAGAAAATCAAATTGGTCTTAGCACAATAGCTCATGCCTGTAACCCTAGCGCTTGGGGAGGTCAAAGAGGGAAGATACTTGAAGCCACAAGTTTTAGACTAGCCCGGGCAACATAGCAAGACCCTATCTCTACAAAAAATAAATTAGCCAGGCATGGTGGTATGTGGGCCAGTAGTCCCAGATACTTGGTAAGTTGAGGCAGGAGGATCACTTGAGCCCAGGAGTTGAGTTAAAGTGAGCTTATTCATTGTGCTGCTACACTTCAGCCTGGGCAATGGAATGATATACTGTCTCTATAGAAAAGGGAAAAAATCAAATTATTGGGTAAAAAATGCAACTCTTTTGTGCTAGAGCTGAGAATAAAACTTTTTACAGCCGTTTAAAGTGTACCTCCTTAAATGGAAGGAGGAATCCTTCAGGGGAGGGAAGGTGTTTACCTTCTTAATAATAAAAGGTCTTTCAATGGAAAAGTATACCTACCTGGGGCATAGAAGGCTGGGAGGGAGGAGTCAAGTTACGGAGCTTTGAAATTTTTTTCATGGCTTTGTATGTTGAAATTTGAAATGTATAACGTGAATGTTGTATGGAATATCTTTGATTTATGTAAAAAAATTTTTTAG
Seq C2 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCACAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(18.3=91.7),PF073187=DUF1464=PU(2.1=16.7)
A:
NA
C2:
PF0007617=RRM_1=FE(53.3=100),PF073187=DUF1464=FE(34.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)