HsaINT0119436 @ hg38
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein cytoplasmic 4 [Source:HGNC Symbol;Acc:HGNC:8557]
Coordinates
chr1:39569863-39571349:-
Coord C1 exon
chr1:39571234-39571349
Coord A exon
chr1:39570003-39571233
Coord C2 exon
chr1:39569863-39570002
Length
1231 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TCTTCATGGTTTCATTTTAGATT
3' ss Score
9.56
Exon sequences
Seq C1 exon
GTGGTGTGTGATGAGAACGGCTCTAAGGGTTATGCCTTTGTCCACTTCGAGACCCAAGAGGCTGCCGACAAGGCCATCGAGAAGATGAATGGCATGCTCCTCAATGACCGCAAAGT
Seq A exon
GTGAGTGTCCCAGTCCGGAGCAACAACCATCGCATGAGCCAGCCGTGGCCCCACCTCGCTATTAACTGGCACACACAAGGCGGCTACTGGTTCTCGGCCCAAGTGTGGCCTGCTCCTACCTCTCCACTCCAGGGCTGGTGAGTCTCCCTGCCTGAGCCGTGGCAGCCCTTTTGACTCGCCAAGGTGGGCTTCCTGCCCAAGCCATGGCCTGCCTGCCGCCTCTCCCTTAAAGGCATCTGTCTGTGGGTTTTGTGAGCATCAACAACTGGGGCTGGCTGGAAAGCAGCTCTAAGCTCACTCTGAGTCGGGGTCTTGGCCAGCGGCAGAGTGGAGAGGGCCCTGGACTGACCAGGAGCTGTATACTAGCAGTGTGACCTTGGCTTTCCTGTGATTCAGGTCTGTCCATGGGTCCCTCGCTAGTGGTTGATGCCAAATTGTCCCCGCGGTTCTCCATTTTCTAACTTATGACTCAGTGACCTAATACAAGGCTGGCTCCACAGTAATACTTGGTGACAATGAAAAAATCCCATCCCTTTGCAGAAAAACTTCATAACAGACCTTGTTGCTTTGATGTGGTTGTTACTGTAGAATGCAGAGAGGGGGAACTTACCAAAGCCATATGGGGAGAAGAAGAGACAATAAGTCTTGGCTATTACAAGCCAAAATAATTTTTGTCCTTTGTGTCATTCAGTATGCCAGAGGATGGGTTATCTTTATAATGTCTGTGTGTGCAGTGGTTGATCTACAGATATCACTAAAAAGAAATACAAAAATGTCAGTGCATGGATAAATTTTCTTTTAAGTATAACAGACCAAAATAAATAAATTTAAAAAGCAAAGGGTGCCCCTTCACTCCAACAATCTCATATCTAGGATTAACCACTGTTAACAGTTTGGTTTGTATCCTTCCAGACCTTTTCTATGCATTTACATAGTTGCACAGAAATGAACATTTTAAAAACATGGCCATCAGGTTTCTTCATGAAGGCAGTGTGATGTGGTAGGAATAGCCCTGGTCTAAGCCAGGAGCCCTGGGGCTGGTCCTCACAGGATAGTCCTGCCTTTTTCTCTTTCTGCTGGGGACTTGGGGTATCTCTGAGCCTCCTTGGTGGTGGATGGGGATCTCGTGTTTTAACCTCTCCTGTCAGTCTTTAACCTGTATTCCTTTGGGTCCCTGGACATCATGTTTTATTCCTCTGGGTAATTACTGTTCTTCATGGTTTCATTTTAG
Seq C2 exon
ATTTGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCTGAGCTTGGAGCCAAAGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGGGAAGAGGTGGATGATGAGAGTCTGAAAGAGCTATTCAGTCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090621:ENST00000372857:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139001=GVQW=PD(7.9=7.5),PF0007617=RRM_1=FE(90.7=100)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
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:
GTGGTGTGTGATGAGAACGGC
R:
AACTGACTGAATAGCTCTTTCAGACT
Band lengths:
254-1485
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