RnoINT0106605 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140988815-140990377:+
Coord C1 exon
chr5:140988815-140988910
Coord A exon
chr5:140988911-140990104
Coord C2 exon
chr5:140990105-140990377
Length
1194 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATA
5' ss Score
8.49
3' ss Seq
CATCCAGTCTCTTTCCGTAGGTG
3' ss Score
9.84
Exon sequences
Seq C1 exon
GGAGTGAATCTCTACATTAAGAACTTGGATGACACCATTGACGATGAGAAGTTAAGGAAAGAGTTCTCACCCTTTGGATCAATCACCAGTGCGAAG
Seq A exon
GTAATAACGTGTGCTAGCATGGGTTTGGAAACAGTTTTTTCTGTCGTTGGGTCAATGGCGTTAGTTAATTGTGTTGGTGGTCCAGAGTACAATGTTCTAGCATGTTCCTCCTTGCTTCAGATATCTGGAGAAGGTTTGTGATTGTATGTGTTGTCTACTTGCACTGGGGCTTGGAGTCTGGCCCAGTTCCTCACAGCACTCAAATCTTTCCCAGGCCTGCTTGCTTGGTGCTGGTCTGGGGACAGGCAGTGCTATAGTAGAGCAGAGGAAATCCAGACGGGTCGTTTCCATCTGTCCTGGGGCCTGTCCCTACAACTCTGCCACACTTCCCCCCTTGAGAACAAGGTTTTAAAGGTTTAGTGGGCCTTTGACAGGAAAGTTTGGCTGGACAGCCAAGATCATGCGGGCATGGTCTGCAACGGGACCTTAGCACTTGGGGAGTGACACTGGTCGAGGTAGTGGCCTGACACTGCATATTGCTTGGTGGAGCACACAGCAGCTACCACACAAGGCCTTTAAGTTGTGAAAAGGGTTGAGTGGTGGCCAGGTAGGGTTTGGCCTTCTGTGTAAGGTGTTGGTATTGGTATCGGTTTTTCGTTGGTTGTATTTTCATACAGGGTCTTGCTATGTAGTCCTGGGTGATTAGAATTCACTATGTAAACCAGGCTGACCCAAAAACTCAGATCTGCTTGCCTCCTGGATGGCTGGCAAGATGGTGTATGCCACTATGCTCTGCTGTGGGTATTTTATTTAAACCTTTTGGGGTGCTGGCAAAAGAACCCTCCTTGCTTCAGATATCTGGAGGTTTGTGATGGGGGGTGGATAGCCCTGGCAAACATTTCCTGGTTCTTCTTGGTGTCACCCACTTAACTGGCCCTGTTGGTGTATGCCTCTGCAAAGCCATATACCTTTAAAGACCAGGCAGATGACAGGGCACTGTTCCATGGGTAGAAGACTGTTGACCTAGTAACACACTGACCTTGGAGGATTAAAGAGGCCAACACACAAGGCACAGGAAAGCAGTAACCCCTTCAGTAAAGAGAAAGACGTTAGAGGCTGGCTCTGCAGAGACTGTGATGTATTCAGAGTTAGTTGTCTTAGAGTGTGGGAACCAGGGCTCAGAGGGGCTGGTAAGACTGATTAGACTCTGTTTTCCTGTCCTGCCTCCCAGTGACATCCAGTCTCTTTCCGTAG
Seq C2 exon
GTGATGCTGGAAGACGGGAGAAGCAAAGGGTTTGGCTTTGTCTGTTTCTCCTCTCCTGAAGAGGCAACCAAAGCGGTCACGGAGATGAACGGACGCATTGTGGGCTCCAAGCCTCTGTACGTCGCCCTGGCCCAGAGGAAGGAGGAGCGGAAGGCTCACCTGACTAACCAGTATATGCAGCGTGTGGCAGGAATGAGAGCGCTCCCTGCCAACGCCATCTTAAATCAGTTCCAGCCTGCAGCTGGTGGCTACTTTGTGCCGGCAGTGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:7
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=0.154
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTGGATGACACCATTGACGA
R:
GCACTGCCGGCACAAAGTAG
Band lengths:
342-1536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]