DreINT0109541 @ danRer10
Intron Retention
Gene
ENSDARG00000017219 | pabpc1a
Description
poly(A) binding protein, cytoplasmic 1a [Source:ZFIN;Acc:ZDB-GENE-030131-3238]
Coordinates
chr16:55142369-55143222:+
Coord C1 exon
chr16:55142369-55142485
Coord A exon
chr16:55142486-55142910
Coord C2 exon
chr16:55142911-55143222
Length
425 bp
Sequences
Splice sites
5' ss Seq
AGGGTTTGT
5' ss Score
3.38
3' ss Seq
TTATTTGCTGCTTGTTTCAGAAA
3' ss Score
9.02
Exon sequences
Seq C1 exon
GTGGATGAAGCAGTAGCAGTGCTGCAGGCTCACCAGGCCAAAGAAGCAGCACAGAAATCAGTGCCCAGTCCTGCTGTGCCCGCCGTCTAACACAAGGTCAGATCAGCATATTAAAGG
Seq A exon
GTTTGTTCACACAAAAATGGACAGTAGTCCACTATTTACTCACTCAAGGCATCCCTGGGTGTTTGTGATATGAAGCTACGGGAAAAAACCTTTCCAGGATGATAGCGGGATAGAACTGTAAAATACAGGAGAATCCTGGGAAAAACCAGAGGGTTGACAGATATGATAAAGGCACATAACATTTATTTAATTCTTCTAGCCTTTTCCATTTCAGCTACAATCTGACATGTGTCGTCTTTAGATCTAGCTTAAATCTGTGCAGTTAAGCGTTAAAGACTGGCCATCATTTAAGTCCAACATGCCATTGTTATGTCTGTGTTTGTAAAGTGGGGGTGACGAGGTTTATTTAGGTGTTTAATCTGTGTCTTTGCTTGACTCTTGTTGGAATGCATCGTAAAGGTGTTTTTATTTGCTGCTTGTTTCAG
Seq C2 exon
AAATGAAGCTCTCCGGCTCTGTCTTCTCCTCGAGGATCGTATTAAAAAAGAGAATAAATATCGAAAAACCAGAAACTCTCACAGAAAAAAAAACACCACCAAATTCAAATCTCTGCCAGGTTGAGAGGCTACATCTTAACCTTGATTTATATGAAAAAACATACAAAAAAATGGAAAACTTTTAATTTTGAAAATGTCAAAACATTCCTTTCTTTTTATTCCTCTTAATGAATGCTCATTGTCAATTGTTCCTGCAGTTGATGCTTTGAACATTTGGAAAAATTACATTGACTTAATAAAAATTTAAACATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017219:ENSDART00000024729:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.931 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=23.3)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACCAGGCCAAAGAAGCAG
R:
GCAGGAACAATTGACAATGAGCA
Band lengths:
344-769
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]