HsaINT0119425 @ hg19
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43552802-43559367:+
Coord C1 exon
chr20:43552802-43552897
Coord A exon
chr20:43552898-43559100
Coord C2 exon
chr20:43559101-43559367
Length
6203 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTGTCTTGTCTTGCTTTTAGGTG
3' ss Score
11.3
Exon sequences
Seq C1 exon
GGTGTGAACTTGTATGTGAAGAATCTGGACGACTCCATTGATGACGACAAACTGAGGAAAGAGTTCTCTCCCTATGGAGTAATTACCAGTGCGAAG
Seq A exon
GTGAGGACTGGGGGCACCTCCGGGGGACAGCGTTCCCCTCCATCCTCTCACCACCATCCCCCCACAACCCCACCCCTCCACCCTCTCGCCCAGCAGCCTTCAGGGGGTTGGTGCCGGCTACCCCTTCTGGGGCTCTGCTGACCCCGTTGGAGCTTGTAGCCATCTGCAGCCTTGTCTGGGCTGGAGGGGAAGAGGGTAGAAATATAGTCCCAGTCACACAGCTGGACTTGGGGCTCACTGTCACCTTGGCATTTATTGAGTGCCTACTGTATGCCAGATTCCAGAAATTCATATCTTAGTATTTCCATTGACTTTTGTTGTCTGGCCTCTGCCAGTGACATTACCCTCCTGGGCCTCCGTTTTCCCATCTGGAAAGTGAGAGGGCTGGACTTCGTCATTCTTCATTTGTTCTTCCCTATTTCTGGAGCACCAATTGTGTGCCCAACCCTGTTAGGCCCCTGAGATGTGGCAACTGGCCCATCAGCAGCTCTATGAGCTTTAGCAGATGTTGTCTTATAGATAAGGACACTGGGCTCACTGGATGGCTTTCCGACCCTGGCTTCTCATTACAACCCCCTGGGCAATTCTTAAATACACACACCTCAGTCAGGCATAGAATGTGGATCCCCGGGGTAGGGCCTGGGCTTTTTATTTTTTTTTTTTAAAGCTCCCAGAGGCTGGGCAATATGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCAGATCATGAGGTCAGGAGATCGAGACCATCCTCGCTAACACGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCATGATGGCACGTGCCTATAGTCCCAGGTATTCCGGAGGCTGAGGCAGGAGAATGGCATGAACCCAGGAGGCGGAGCTTGCAGTGAGCCAAGATCGTGCCACTGCACTCCAGCCTGGGCAACAGCGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAGCGCCCAGATGGTTTTTAAGATGATGATCCAGTGTTTCTTCATTCTATACTTAAATACCTGCTGTTTTACCAGGCTCTGTGGGAAACAGGAGCAAATCAGATGTGATCCTTGCTTTCAAGTAGCTTATAGTCTAGTGAGGAAGTCAGCCCGTCACTAACTCAAATGGATTATAAGATGGGGGACAGTATGGGAGGCAAAGCTACAGGAGTTCAGTGGAACAGAAGGGAAGGCTGCCTGGAAGAAGTGGCAGTAGCAGCAGTGTTTGACTTGGCTGTGAGGAGGTAGGGAGCTGGAGTGGGAATGAGGAATTTTCCAAAGAGATCAGTGTGAGTGACAGGATGGGGGGACCCGCCTGAATGATGTGATGTTGGGTTCTGAGGAAGTGGTCTAGAAGTTCTCTTTTGGCTACTGAGTCCAGTTGTAAACATCCTTCAGGGAGCCTTGTGTTTGGAGGAAAAAAGGTTGTCTTTTAGGTTAAGATCCTTTTGAAAAATGCGAGAGAAGGCTGTGGCACATGTAAATTAGGCATCAGTAAATTTGATTACACATCATAAAAAGCTATAGGTCCTCTTTCCAAGCAAATGCATATACATTTGATGTAGAAACATGGTTGAAAGCTGGAATTTTAAAGTTAATCAGGTTTAAATGTAAACCCCAGTCCTACCATTACCTAGCTGTAGAAACTGAGGCAAGTGGCTTTGCTTTTCGGACCTTGTTTACTCACCTATAAAGTGGGAGCAACATTTCTCACCTCTCCAGGTGTCCTAAGAACTACTAAAGAGGCTGCATGTACAGCATCTGCATTCAATAAGTAGTGAAATAGTGATTGTCGTAATGATTCATCATACACCTTGCATACAGCTTCAGGAGATGGACCTTCTTGAGGACTCCCCGAACAAAGGAAATGTGTAAATTTGGATTGCTTAGAGTTAAGGCACACCTGGGGTGACCATCTTTTTAACAGGACAAACGGTATAAAATGGGGATTATAAATATATCTATTTTTTGTGTGTGTGATGGAGTCTAGCTCTGTTGCCCAGGCTAGAGTGCAGTGGCGCCATCTCGGCTCACTACAACCTCCGCCTCCCGGGTTCAAGTGATTCTTCTCCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACCTGCCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTGTTGGCCGGGCTGGTCTCAAACTCCTGACCTAGTAATCCGCCCGCCTCAGCCTCCCAAAGTGCTGCAATTACAAGAATGAGCCACCACGCCCAGCCTACATATATATATATATTATACAATTATTTATTTATTTTGAGATAGAGTTTCCTTCTTGTCGCCCAGGCTGGAGTGCAATGGCGCGATCTTGGCTCACTACAACTTCTGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTTCTGAGTAGCTGGGATTACAGGCGCCCGCCACCAAGCCCTACTAATGTTTGTATTTTTAGTAAAGATGAGGTTTCACCATGTTAGCCAGGATGGTCCTGAACTCTTGACCTCAGGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTGAGATTATAGGCGTGAACCACTGTGCCTGGCCTATGTTATGCGATTTTATATATTTTGGTTTATTATTATTTTTTATTAGATGCAGGTTCTTATTCTGTTGCCCAGGCTGGAGGGCCATGATGTGATCATGGCACGCCACAACCTCAACCTCCTGGGCTCAAGTGATCCTCCCACCTGAGCCTCCTAAGTAGCTGGGACCACAGGCATGTGCCACCATGCCCAGCTGATTTAAAAAAAAATTTTTTTTTGGTAGAAATTGGGAGTCTTGCTGTGTTGTCCAGGCTTGTCTTGAACTCCTGGGCTCAAGCAGTCCTCCTACCTCAGCCTCCCAAAGTGCTGGGATTATAGGCATGAGCCACTGCATCTGGCCTGTATTTTGTTTTATATAAAAATAATTATGAAAATTAAAGGAATTAATGGATATAAATACTTATACCACTATCAAGTTCATGGTAAGCTCTGCATAAGTGTTAGCTTTGCTAAATTTTATCATTATTAACTACCGACTGCCAGAAGTTCTTAACAATATATATATATTTTTTTTTTTTTGAGATGGAGTTTTGCTCTTGTTGCCCAGGCTAGAGTGCAATGGTGCAATCTTAGCTCACTGTAACCTTTGCCTCCTGGGTTCAAGTGATTCTCCTGCTTCAGCCTCCTGAGTAGCTGGGATTACAGGCGCCTCTCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTGTCACTATTTTGGCCAGGCTGGTCTCGAACTTCTGACCTCAGGTGATCCACCTGCCTCAGCCTCCCAAAGTGCTAGGATTACAGGCGTGAGCCACTGTGCCCGGCCCTTTGGCTATCTGATGAAGCCTGTGGAACCCTTCTAAGAATATTTTTTAAAAACTTTTTTGAGACAGAGTCTCGCTCTATCACCCAGGCTGGAATGCAGTGGTGCCATCACAGCTCACTGCAGCCTCCAACTCCTGGCCTCAAGTGATCTCCTGTCTCAGCCTCCCAAGTAGCTGAGACTATAGGAGCACCACTATGCCTGGATAATTATTTTTTATATTACCCAGGCTGGTCTCAAACCCCTGGGCTCAAGCAATTCTTCCGCCTCTGCTTCCCAAAAATAGGCATGAGCCACCAAACCTGGCCCTAAGAATATTTTTAAATGCATAAAATAAGATTCTTAGGTGTACAAAAAAATCATACTGAAAAAATATAATGGTCAAAATACTAAAGTGAAAGCAGTATGTGCTTCTTTTATTATTTTTATTTTTATTTTTTTGAGACGAAGTCCCACTCTGTCGCCCAGACTGGAGCGCAGTGGCATGATCTTGGCTCACTACAACCTCTGCCTCCCAGGTTCAAGAACCTGGGTTCTGCCTCAACCTCCTGGGAAGCTGAGATTACAGGCACCCGCCACCATAACCAGCTAATTTTTGTATATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATAAGCCATTGCGCTCGGCTGAGATTAGCAATAATTAATGTGATATGAAAATATTTTCTTTTTCTTCATGACAAATTCATGGCTAATACTGCCAGGATTTTTTTGTTGTTGCCCATATTCATAATAGAAGGAAATGCTAATATGAAAATAAAGATGTCACTTTTTCCCCAATCCATGCAATTTCCCCCTAAATTGTATCCATGACCTACCTGAGGGGGATCCATGGACTCTCAGGTTAAGACCCCTCTACTGAAGGGTAGCAGAGTACAGTTTCAAAATTACTGATTAAGAGCGTGGGCTCACCAGGAGTTCAAGCCCAGCCGGGGCAACAGGATGAGACCTCATCTTTACAAAAAATGAACAAAATTAGGCATGGTGGTGCTTGTCTGCAGTCCCAGCTACTTGGGAGACTGAGTTGAGAGGATCACTTGAGGCTGAGAGGTTGAGGGTGCAGTTGAGCTGAGATTGCACCACTGCACTCCAGCCTGAGTGACAGAGTGAGATCCTGACTCAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAGGAAAAAAAGAAGATTTTAAAAATAACTCTAGTCCTTATGGGCTGTATGAGCCAGGCCGGTGTCTTCACCCTAAAAAAAGGTTAAAAACCCAGGGCCAGGTGTGGTGGCTCCTGCCTGTAATCCCTGCACCTTGGGAGACCTAGGTAGGAGGATCTCTTGAGACCAGCCTGGGCAACATAGTGATTGCTGATCTCTACAAACTTAAAAAAAAAAATTAGCTGGGTGTGGTGGCATGTACCTATAGCCCTAACTACTTGAGAGGCTGAGGCAGGAGGATCCCTGGAGCCCGGGAGTTTGAGGCTGCAGTGAGCTATGATCATACCACTGCACTCCAGCCTGGATGACAGAGTGAGACCCCATCTCTTTAAAAAACAAACAAATAAACAAAAAGACAAACCCTAAATGCCATGTGGGTTGGATCCTGGAAGAGAAAAAGAATATTAGGGGAAAAAAGAGTGAAATTCCAGTGAAGTCTGGAGTTCAGTTAATAGCATTGTAGTTAATAGGAGCTAATGGTATAAAATAGTTAATAGCATTGCACCAGTGTTAATTTTGTAGTTTTGAAAAATGTACCATGTTCACATTGGGGGAAACTGGGTGAAAGATATACAGCAGGCCAGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTCTCTCTACTGAAAATACAAAAATTAGCCAGGTGTGGTGGCACACGCCTGTAGTCCCATCTACCCAGGAGGCTAAGGCAGGAGAATTGCTTGAACCCGGGAGGCTGAGGTTGCAGTTAGCCGAGATCGTGCCACTCCACTCTAGCCTGAGTGACAGAGTGAAACTATGTCTCAAAAAAAAAAAAAAAGATATATAGCAACCCTCTGTACTGTTTTTGTAACTTTTTCTGTAAATCTAAAGTTACTCCAAAGTAAAAAGGTTATTTTAACAAAAAGGCTAAGAACCTCTTCCCCAAATTCCTAAAGAACTTGGCTTGGTACTTAGCAGAGGCGATAGAAGCTTACCAGAACAATGTGTTGGGTTGAGTCCTGGCTAACGTATGAACCACAGGCTGAGTGACCCCAGACAAGTCACTCTTTCGAGTCTCTCTTATCCCGGCTGTAAAGTGGGAGCCGCGATGCCTCCCGCATCGGGAGGTTGTACATGTGAGGTGTGAAGACATGTAAAGTATCTGGCATGCAGCAGGCCTCATAGATGGGGGTGCGTGCTGCATCCCTCAAACAGCTCAGTAAACAGGGTGCACGCTACATCCCTCCATCACTCCTCAGTAAATGGGGGTGCACGCTACATCCCTCCATCACAGCTTGCTAAACGGGGGTGCACACTACATCCCTCGAACACAGCTTAGTAAACAGGGGTGCACGCTACATCCCTCCATCACAGCTTTCTCGCGGGCCTGCCCAGTGCTGGGCTTAGCCCATGGGGAGGAGGGAGGCAGCGCAGCCCCAGGAGCCTTCCTTCCCCACCCCAGCAGCTCTTGTCTTGTCTTGCTTTTAG
Seq C2 exon
GTGATGACAGAGGGTGGCCACAGCAAGGGGTTTGGCTTTGTGTGTTTTTCCTCCCCAGAAGAGGCGACAAAGGCCGTGACAGAGATGAACGGGCGCATCGTGGGCACCAAGCCACTCTACGTGGCACTGGCCCAGCGCAAAGAGGAGCGGAAGGCCATCTTGACCAACCAGTACATGCAGCGCCTCTCCACCATGCGGACCCTGAGCAACCCCCTCCTGGGCTCCTTTCAGCAGCCCTCCAGCTACTTCCTGCCTGCCATGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-PABPC1L:NM_001124756:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.120
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(82.4=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
- Genotype-Tissue Expression Project (GTEx)
- 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)