DreINT0109564 @ danRer10
Intron Retention
Gene
ENSDARG00000002597 | pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:ZFIN;Acc:ZDB-GENE-030131-5836]
Coordinates
chr8:45339301-45340550:+
Coord C1 exon
chr8:45339301-45339417
Coord A exon
chr8:45339418-45340416
Coord C2 exon
chr8:45340417-45340550
Length
999 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TGGTTTCTCTCCTGACTTAGCCA
3' ss Score
5.04
Exon sequences
Seq C1 exon
GTCCATTTCCAGCTCAGTTTGTGAGGCAAGCAGTGCCACGGAGGCCCTCCACTACCATCAGCACTGTCCGCCAGGCCTCCACTCAGGTTCCTCACATAAACAACACCCAACGAATGG
Seq A exon
GTAAGGCAGTGTCCATGTTTACATAATACATTGTGATCTTGTTATGGGGAAAATGCTGTACTAGTTGTTGAAAGTCTGTATCCCTGTTATATATTTAAAACGGAGATTAAATGCCTACTATATAATGTACAGTATGATATACATATGCAATATTATAATATACCGTACCAATCTCAGTCCTGGAGGGTTGGTGTCCCTGCAGAGTTTAGCTGCAACATACCTAGACACATCTGACTGGAAGTTTTAATTATACATTATAAGACCTTGATTAGCTTGTTCAGGCGTGTTTGATTAGGGTTGGAGAAACTCGGCAGGACATCGACCCTCCAGGAACAAGTTTGGGGACTGCTAATATACAGTGGTGAACAGAACAAATTTGTGAAACTTTAAGACGAGAGAACTTTTAGAAGAACTTTGATGTTTTGATCCACTTTAAAAGTTGACTAGATTTTGTTTGTAAAAAAAATATTGTAATATTGTATTTTAATATTTCATGGTCATTCTGTATTAAATAAATTTTATATGGGATACAAAATCATAAATTGATAAACGCACTTTATACTGATTGAAAAAACACTGAAGCGTGTGCAACCTGACAACCTCGAATGAAAAAAATATAGATGAACCGTCATATTTACAGTTTTTTTCTTTTTCATTTTTTTTGCACTGTTTAAATGAAGAAATTAGTTTTTTTTTTAGTTCATTGAAAATTGCAATATTCAAGTGTAATTAAGAATCTGCTTAGCTTTGTGCGCACGTGTATAATTAATATTTTGTTTCACCAATTAAATCATTGAAATGCAGCACAAAATATGAACATTTAGTTTAATGGTGGGTAAAATATGAATTTTCCTTGGCTGTAACTCACTTTTGCCACACTAATTTTGTATGCGTTTATTTGTATAACATGGAGTAGAGAGTAATGCCATTATTGTTTTTTGACAGAATTTGAAATGCAATTTTATTTATTTATTTTTATTGGTTTCTCTCCTGACTTAG
Seq C2 exon
CCAACATTGGGACCCAGACTGCAGGCGGGAGAGCTGCGGGAACTGCAGTCAGAGGAGTCAGCCAATACAAGTACTCAGCAGGGGTTCGAAACGTGCAACAGGTCATTAATGCCCCAGCTCCTGTTGTTCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002597:ENSDART00000134161:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=0.342
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCATTTCCAGCTCAGTTTGTGA
R:
GATGAACAACAGGAGCTGGGG
Band lengths:
248-1247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]