HsaINT0119436 @ hg19
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]
Coordinates
chr1:40035535-40037021:-
Coord C1 exon
chr1:40036906-40037021
Coord A exon
chr1:40035675-40036905
Coord C2 exon
chr1:40035535-40035674
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-PABPC4:NM_001135653:3
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=FE(55.1=100),PF0227010=TFIIF_beta=PU(2.4=10.3)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8),PF0227010=TFIIF_beta=FE(28.0=100)
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
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)