DreINT0109577 @ danRer10
Intron Retention
Gene
ENSDARG00000059259 | pabpc4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:ZFIN;Acc:ZDB-GENE-030131-9663]
Coordinates
chr17:25298279-25299722:-
Coord C1 exon
chr17:25299607-25299722
Coord A exon
chr17:25298419-25299606
Coord C2 exon
chr17:25298279-25298418
Length
1188 bp
Sequences
Splice sites
5' ss Seq
GGTGTGAGT
5' ss Score
6.05
3' ss Seq
TGTCTGCACTTTTTTTGTAGGTT
3' ss Score
10.19
Exon sequences
Seq C1 exon
GTGGTGTGCGACGAGAACGGATCGAAAGGCTATGCCTTTGTGCATTTTGAAACTCAGGACGCAGCCGATCGTGCCATTGAGAAGATGAATGGAATGTTGCTGAACGACCGCAAGGT
Seq A exon
GTGAGTGTCTGAGCATAACCTTAGTCATATGAAAGGAAGGAGGAGTGCTGGTTTGATGAGCGACAGCGATGCTCAAGAGAGACATTTTGGGTGATCAATTAAAGTTAAAGGATCAGAATCATTTACTGAACTTTCAAATATATTCTGACTTTTAAAAATCATTAAACAATGAAATAAAAAATGTACATACAATTAAAAGCCAATTTAATTGGATTAGTGACAAATCTCCATCACTTAAGGCTGGCACAAGATCATTTTTGAGTTAAATCCCCTGGAACACCTTGTATTGCCATGTATTAGACAACAACAGGCCACTTTTTTCAAATTTTGGACTTATGTTTGGGTTATTTGAAACCTAGTCCCTACTGCCTATTATTTTTAATGGAATGTTGTAATTGCATTACTGTCTGGAAAATCAACAATATTGTAGGCCTTTTTCTAGGGGTACTCATGTCTTATATACAATCTAAGTTTCTTGGTTTATTTACTTTTTGAAGATGTTATCTGTTTCCGATATATTTGTATTATATGTGTATTATTGTAAAACAAATCTTTCATTCATTCAATTTTCTTTTCAGCTCATTACCTTTACTAATCTGGGGAACCATCACCATCTTATCCAGCACATGTTTTACGCAGCGGATGCACTTGCAGCCGCAACCCAACACTAGGAAACACCCATACACTTTTGCATTCACACTAATACACTATGGCAAATTTAGCTTCTTAAATTCACCTGTACTGCATCTCTTTGGACTGTGGGGGAAACCAGAGCACCCGGAGGAAACCAACACAAACACCGGGAGAACATGCAAACTCCACACAGAAATGCCACCTGACCCAGCTGAGGCTCGAACCAGCGACTTTCTTGCTATGAGGCGATTGTGCTACCCACTGCGCCACCTTGATGCCCCTAAAACAAATCAATAAACATAAGTTATAATGAGTTTAAATAGTGATTTATAATATATATAATATGAAACCAATTGAGCTCAGATTTAATTTGTACCTCACCGACTGTCAATGCATGTACATCAACAGTTAGTTTTCCAACATTTTAGTGTTTGTAAGTCACACTTGTCTCTGCTGCAGCTGGTATGAGTCAACAGTTGTTCTGCAGCTGTCACTCCACTGAGTCTGTATTGCATTTCTGCATGAGTCACATTTATGTCTGCACTTTTTTTGTAG
Seq C2 exon
GTTTGTGGGCCGTTTCAAGTCCAGGAAGGAGAGAGAGGCAGAAATGGGTGCCAAAGCCAAAGAGTTCACTAATGTTTACATCAAGAACTTTGGCGATGACATGGATGATCAGAGACTGAAGGAGCTCTTTGATAAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059259:ENSDART00000082327:3
Average complexity
IR
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)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTGTGCGACGAGAACG
R:
TATTTATCAAAGAGCTCCTTCAGTCT
Band lengths:
254-1442
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]