DreINT0109544 @ danRer10
Intron Retention
Gene
ENSDARG00000017219 | pabpc1a
Description
poly(A) binding protein, cytoplasmic 1a [Source:ZFIN;Acc:ZDB-GENE-030131-3238]
Coordinates
chr16:55127963-55129240:+
Coord C1 exon
chr16:55127963-55128102
Coord A exon
chr16:55128103-55129145
Coord C2 exon
chr16:55129146-55129240
Length
1043 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
ATGTTCCTCTGTGTGCTCAGGTC
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTTTGTGGGTCGCTTCAAATCCCGTAAGGAGCGCGAGGCAGAGATGGGCGCCCGTGCAAAAGAGTTCACCAACGTTTACATCAAGAACTTCGGGGAGGACATGGATGACGAGAAGCTGAAGGAGATCTTCTGCAAATACG
Seq A exon
GTGAGTGTTTCTCTCTGATAGTGCATGGTTTTGTTCTTTATCAGGGTGTCAGCAGGATCTTGCTCACACCCCAACTGCAAAAGAACTCAGATTAATCAACCTCATTTGAGACTGTCGTCTGCGATACGTCTTTTGTTATTATTATAACTTGACAGCAGAGTTCTATTAATGACCGTATGATATTACAGTATCATAAATTTAACAGCATTTAATAAAACCTTACTAAATGTCTGAATCACACCAAGGGTGCTTGAGGGTGTATAAAATCCATAATTCTGAATGTGGGGTGAACTTTTTGAGTGGAGCAAACTGATACTGATCATTGCATCCATTGTAAATACTTCAATAAATATTGACCCCTCTGTATTAGGGGTCTGAGATCACCTTGTTTGTTTACATGTGCATTCTGAATCGCTTTGCATTTGAAGGGGTTAAATAAACTAGCTGTGTAGTTTATGAAGTTGATAAAATCCTGCTAGATTTACTGCAGTGACTAAGCCAGCGTGGTTATTCCTGCTGTTCTGTTGGTGCCCCCTGCTGGATTAGCATTTAATTCAATATAGAAATGTTTTAGTCCTATTGGTGAAGTTTTTTTCCTCTCCGCTGTCGCCTCTGGCTTGCATGGTTCAGGATCTGAAAAGCTACTCATTGATGAACTTGCCCTTCAGTGTTTGGACTCTCAATGATGACTTTAAACCACACTGAACTGAGCTAAACTGAACTGAACTTAAACACTAAAAACTGAACTACTCTGATCCAGTTACTATGACCATTTATGTGGAGCTGCTTTGACACAATCTACATTTTAAAAGCGCTGTACAAATAAAGCTGAATTGAATTGAATTGATATTAGGATTTCTTACAGTGAGCGTTTAGTGAATATACTGGTTAAAATGTGGCCAGTGTTACTGGTTAAATTGGTGCAGTTCAGCTTTAAAAAGAGTCTTAATAAAAGATGTTAAAGGTGTTCAGTTTCACTCTGGTTCCTGTATATACTGTGTTCATGTATGAATCTGATTTCTGATGTTCCTCTGTGTGCTCAG
Seq C2 exon
GTCCAGCGCTGAGCATCCGCGTTATGACTGACGACAGCGGCAAATCCAAAGGTTTTGGTTTCGTGAGCTTCGAGAGACATGAGGATGCACAGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017219:ENSDART00000024729:4
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=0.052
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTGGGTCGCTTCAAATCCC
R:
CTGTGCATCCTCATGTCTCTCG
Band lengths:
230-1273
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]