HsaINT0119417 @ hg38
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein cytoplasmic 1 like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr20:44936637-44938191:+
Coord C1 exon
chr20:44936637-44936730
Coord A exon
chr20:44936731-44938060
Coord C2 exon
chr20:44938061-44938191
Length
1330 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TTAGAAGGTGTTCCACACAGGGG
3' ss Score
2.14
Exon sequences
Seq C1 exon
GTCCAGGAGCCGGCTGTGCACATCCCAGGACAGGAGCCCCTGACCGCGTCCATGCTGGCTGCGGCGCCCCTGCATGAGCAAAAGCAGATGATTG
Seq A exon
GTGAGTGGCTGGTTCTCCTACTGTGGAGCAAGAAGAGGAGGGCTGCGAGCTGGCTAGCCTGCTGGGAAACACCTCACCTGGTGGTCCAACGTGAGGTCAAATTCCAGCTTTGTCACCGACCCCCCTACTGGGTGACCGTGGCCAAGCTGGCTCTATTCTCTAGGCACCTGTTATCTTGTCTTAAAACGCTGGTCAGACTGGATGGTCCTGAGCTTTCTTCCACTGCTGCTGTCCTGTGACTTTGAGGTTGGGAGACAGTCCAGATGTGGGGAGATCAGGGGACAAAGGGAGGAGTAGGGGTATGGTCTTGGGTTTCTGCTGAGAAATGGCTTGTAGGTGGGGGGTTAAAGTTCCTCACACCTCTCCTGAACGGGAGGAAGCTGCTGTTCACCAGTTTCCAGTGCTCAATGCGGGCAGGTGGGGCATCTGTGCGTTTGGTAAATACATGATGTTTCCCATAGATTCTGGATTCCTTGTGCAATTCATCTTCACCCCTAGTGTCCATGGCAGGCCCTGATAAAAATGCCACTAAGTGAACACAAGCTTGTTCCTGGTTGGCAGGTTCTTTACTGCATGGCCCCCGAGACCTCCAGACCCTTTACTGAAGGCCCCCATTACCACTGCCCCATTGTTTCCTCAGCTTACTTAGGGTTTTGCCACATTACCCCTTCCCCTCACCCCGAAATTTTTTTTTTTTTCCCTGAGATGGAGTCTTGCTCTGCTGCCCCGGCTGGAGTGCAGTGGCACGATTTTGGCTCACTGCAACCTCCACCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTTCTGAGTAGCTGGGCTTACAGGCACATGCCACCATGACCAGCTAAGTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTTTCAAACTCCTGATCTCAGGTGATCCACCCACCTCAGCCTCCCAAAGTACTGTGATTACAGGTGTGAGCCACCATGCCTGGCCTCACCCAGAAACATTTTGAATGAGCTTAATGGAAGTAGAAGTCTTTGTTAGTAGTTCTCTGTAAACATTTTCACTTTCTTCATGGGACGATCCTTTCCGCCCCCACTTAAGGCACCCAGTCCTGGCTGGGCCCTGGACACATTGCTGAGATGGGCTGACCACCAATACCAGGCCCAGTCATTAAAAGTACCTGATGTTAGAAGATCAAGTGTTAAATGTCATAGCCTAGAAGGAGCAGTTCTGGGAGAAGAACCCAGATGTCCTCAGTGCTCCACTCCATACGAGCCCTGGGATGCTGGGGTGTGAGCTAGGCCGTGCACAAGCCATTAGAAGGTGTTCCACACAG
Seq C2 exon
GGGAGCGTCTCTACCCCCTTATCCATGATGTCCACACCCAGCTGGCTGGCAAGATCACGGGCATGCTGCTGGAGATTGACAACTCAGAGCTGTTGCTCATGCTGGAGTCTCCAGAATCCCTCCATGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104:ENST00000217073:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.409 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=62.5)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGGAGCCGGCTGTG
R:
TTGGCATGGAGGGATTCTGGA
Band lengths:
224-1554
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