HsaINT0119400 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101730315-101734315:-
Coord C1 exon
chr8:101733619-101734315
Coord A exon
chr8:101730509-101733618
Coord C2 exon
chr8:101730315-101730508
Length
3110 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TGAAAATGTCCTTCCTGCAGCGG
3' ss Score
9.22
Exon sequences
Seq C1 exon
CCCTTCTCCCCGGCGGTTAGTGCTGAGAGTGCGGAGTGTGTGCTCCGGGCTCGGAACACACATTTATTATTAAAAAATCCAAAAAAAATCTAAAAAAATCTTTTAAAAAACCCCAAAAAAATTTACAAAAAATCCGCGTCTCCCCCGCCGGAGACTTTTATTTTTTTTCTTCCTCTTTTATAAAATAACCCGGTGAAGCAGCCGAGACCGACCCGCCCGCCCGCGGCCCCGCAGCAGCTCCAAGAAGGAACCAAGAGACCGAGGCCTTCCCGCTGCCCGGACCCGACACCGCCACCCTCGCTCCCCGCCGGCAGCCGGCAGCCAGCGGCAGTGGATCGACCCCGTTCTGCGGCCGTTGAGTAGTTTTCAATTCCGGTTGATTTTTGTCCCTCTGCGCTTGCTCCCCGCTCCCCTCCCCCCGGCTCCGGCCCCCAGCCCCGGCACTCGCTCTCCTCCTCTCACGGAAAGGTCGCGGCCTGTGGCCCTGCGGGCAGCCGTGCCGAGATGAACCCCAGTGCCCCCAGCTACCCCATGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACCGAGGCGATGCTCTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCCGCTCCTTGGGCTACGCGTATGTGAACTTCCAGCAGCCGGCGGACG
Seq A exon
GTGAGCGCCGGGCTCCGCGGTCGGCCGGGCGGGCGGGCGGCCATGAGGCTCGGGCGGCGGCGGCGGGCGGGGTAGGCCGGCGGGCCCGGGGAGGGGGGCGGGAGGGCATGTCACCCCGCGACGGCCGGCGGGAAGGCGCCGGGGTCCCTGGAGCCGCGTTTCCCGAGCCGGCGGGGACCCGCGCTGCCGGCAGCCACACGCCCGGCTACTTCCTCCTTTGCGACCATTTTCTCGGCCTCAGACGCTCTCAAACTTTAGGGTGATGACGCGCCGGGAGGGTGGGTGAGATTCGGTTCCTCCGCGGCGCTCCCGCCAGTGGCCCCGGGATTCTGGGGCGTTGAACGCTGAGCTCCTTCCGTGGGTAAGAGGTGGAGGCGCTCCCACCACCCGGAGCTCCTGCCGGCGCCCCAGCCTGGGGAGGAAGTGCAGTTCTGTGCTCGAAAAATACCACGTGTTGAACCCTGTAACCTCGCAGGCCCGAGGCCTGCTTCTGCTCCTGCTCCTGGCCCAGTCGCCTGGGGGAGCCACCAGGCCTTAGGATAAAGTTCCTGTGGCGATGTGTGGTGTGGTGGTGGTCCTCAGGCTTGTGAGTCCACTTCCCAGAACTCATCAGTGACTGATGGATCTAGGAATGGAATTTACCGGAGACATGCATTTGGGGTTTCCCCTAGATCAAGCATTTCTCTAACATTAAAAGGGCAGAGTGGGAGGAGGGGATGTGGCAGCCGACCACTTTGAAGGCCAGTTTTCTCAGGCAACTTAGACCATTTTTAGTCAAATTTTATCTTAGATTCACAGTACTGGTGGTTTTCGAGTATATTATGTTACCTTCTGAAATAGTTCCTGTCGTTTTGAGGGGCTTTTCTTTATAAAATAGTCAACTTTGGCTATAAAATGTTACTTTAGTGTAATTCCAACTGGACCAGTCTTATCTGTAGCATGCAAGAAGTTCAAGTTTCTCTTTTATTTTTAAAAGTGGCCCATGATACCTGTAAATCTTGGGAAATGACTGAGTACAAAATAACGGAGATTAAATTGAGCTTGAAATTTATGGGGGAAATGCAGCTAACTTTGTGCTTTTATTTTGAAGCTAAACAGTTAACAGAAACACAATTTTGTAAACAGATAATATCTGTGGTCTGTTGAGTTGCTAGGATTTGTCTTTAGATCAATTGGCTTTGAGAAGTCAGCTTAATTCCATTTTACGGCCCAATTTTGCCTTTTTCCCCCCCTACAGGCTGGCCACTTGAATACATGTCAAATAATCGAAATATGAAGAATTCATTTTTATTAGAAAAGGCCTTAAGGGTGGAATTTAAGCTCCTATTAACATTCATTCAGTAGAACTTAGGTTACTGATCAGCTCTTCACTGTGTAAAGTTGATACTGATTTTGGAAGCAGAATATTGAGTGACACAGAGCCAGAAGTTGTAAAACTGCACTGCAGGTTTCCTGCCCTTTTGCTCTGTAAGCAGTAACTCCAAATGTCACTTCATAACAGTTCTTGTCAACCTTAGGCAGGATGTATCAATGCATGTCAGATGGGGGTAGATAACTTTGGGGCAGGTTATCACAACCTAAGAGTTGGTGGAGAAAACATGGGAATGAATTCTAGAGACCACAAAATGAAAACTTGAAAGTGTTACTCTTTCTCAGCTTAACGTTTTTAAATCCAAAAAACAATTTTTACATTTCTTGGGATTCGAAGAGTTGAACTTCAGGTTGCCGTGGTTACAGTGTACAGTATATATTATCAGTCTGTACCAGTAGACCAGTACCCTAACTACTGAAAAGAATATGGCAGTTTTCCATTTGTCTAGTTTCTGTATGTACAATTTACTATCCAATTAATTACTTAAGTGGATTTCTTGTTCTTTTTTAAAAACTTATTGCTACATTGATAGGCAGAATAGCTTCTGAAAGTGACCAGTTTTCAATTTCATAGGAAGAGGTGACTCATTGAAAAATAGCTCAAGCAAAGTCAGCTAAAAAAAAAAAAAAACTAGGGAAGCTGAGTAGGTGTGGTCAATTGATAATGAGCTAACAGCTGATTATCACTATATTCTAGAAACTGGAACTTTCATTTATAAAAAAAGAGGTGGCCGGAAAATTCATCCTGTCAATAACTTTTAAATTTACATTGGCATGGAATTTGTAGGAATTGTTTCAGGGCTTAAAAGGGACCGTTTTCCCTCTCTTCGGGGACTAGTCTTTTTATTTAAGGATGTGTTATTTCATTTAGAGCCTTTAATGGTACAGGTATACATAATTCAATCCTTTATAGATCCTGAAATTAATTGTAGATTTTGAAATTTTCTAGCAGTATTCAGAAATAACTAAATCAGTTGTTAAGAAAATCAGCGATCTAAAGTGAAATTGATTGTATGTGTCAAGAGAGCGTTAATGGTGATTTCTGAATATTGCAGACCTGGTGTTTTTAAAATTCTGTGATTATGAAACCAAATATGTCTAACTTCACATTAGCTTTTGAAAGCATGATTCAAATCTTGGTCTAGCCTTTCATTTTCTTAAATGGAAGTTGTGCCATGAATCACTGAAACCCTCCCTCCCCCCAATAATTAAGAAACTTTCATTTTTTAGGAAATGGACTAGTTTTCATATAATATTGTTAGTTATTAGCAATGAAATGACCAATTTTAGCAAGTAGTTGGGAAGAAGTTAAAATATTTAAATCTATAAACTACTTCCAGCTTGTAGATAAATCTGTTGCGTAATGTCTTTTATACTGCTTATTAAACAGATTGTATGTGAAGGAATTTGGATTTTGATAACTAGGAAAAAAAGTGCTTTAGATTTAATGGCAATTAAGGCGAGAGATTGCGTCAAGAATTTATTAATTATTAGCAATATGGAATTCTTTTATATGTGAGAAATTTCGGGGGCTTCTGGTATTTGTCTTTGCTTTATACAACTTAGGTCCCACACTAGTGTGTGATACTTGAAAGGTCTAGCCATCTTGAAGCTTAAAGAGGAAGCGTTCAACTGTGAGACCATGTGTCCTCCCACTCCAGTCACCATAGTTTATATAATCTTAAGTAGCCAGCAAAAATTTTGAAGTAATATTGACTCTGAAAATGTCCTTCCTGCAG
Seq C2 exon
CGGAGCGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGCAAAAGTGGAGTAGGCAACATATTCATTAAAAATCTGGACAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.002
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(47.4=27.7),PF150631=TC1=WD(100=87.7),PF0007617=RRM_1=PU(52.8=43.1)
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)