RnoINT0106601 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140985315-140986673:+
Coord C1 exon
chr5:140985315-140985430
Coord A exon
chr5:140985431-140986533
Coord C2 exon
chr5:140986534-140986673
Length
1103 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TCTTCGTGGTTTCTTTGTAGGTT
3' ss Score
9.76
Exon sequences
Seq C1 exon
GTGGTCTGTGATGAGAACGGCTCTAAGGGTTATGCCTTTGTCCACTTCGAGACCCAAGAGGCTGCCAACAAGGCCATCGAGAAGATGAATGGCATGCTCCTCAATGACCGCAAAGT
Seq A exon
GTGAGTGTCCCAGTCTGGAGCGACAGCCATCGCATGAGCCAGCCATGGCCCCACCTCGGTATTAACTGGCACACACAAGGCGGCTACTGGTTCTCTCGGCCCAAGTGTGGCCTGCTCCTACCTCTCCACTCCAGGGCTGGTGAGTCTCCCTGCCCGAGCCATGGCAGCCCTTTTGACTTGCCACAGTCGGCTCCCTGCCGAGCCATGGCCTGCCTGCTGCCTCTCCCTTAAGGCATTCATCTGGGTTTTGTGAGCGTCAGCAAGTGGGGCTGGCTAGAAGACAGCTCTGAGCCCACTCTGAGCAGGGGTCTCGGCCAGCGGCAGAGTGGAGAGGCCCTGGGCTGACCAGGAGCTGGATATTAGTTATAACCTCAGCTTTCCTTCAACTCATTCCTACCCGTGGGGCTCTTGCTAGTTTTTGGCACCAAATTGTCCTCTAGTCTTTCCTCTGAGCTGTGACATTTCACTGTCCGTTGTTTAATTGGCATACTGTGAAAAAAAGCTCATCCCTTTTCGGATCATTACTGTGGGGTTGGGGACAGCCATGGGTATTTTTTTTTTTTTTTTTTTTTTTTTTTGCATTTTGTACTATTGCATTTTGGCTATTACAAGCAACAATCATTTCTGTCCTTTGGGGTGTGGAATAGGCAAGGCTTCGTGTATGTCTGTGTCGGGTGTGTGGACATATTTTCCTGTCAAGGTTACCGAATGATAAGCAAAGGTCACCTGATTGCGGCCGTCCCGCTGCTGGACTTAACCACTGTTAACAGTTTGGTTTATATCCTTCCAGACGTTTTCTATGCATTTACATAGATGCACAGAAATGAACGTTTTAAAAACATGGTCTTCTGGTTTCTTCACGAAGGCAGTGTGATGTGGTAGGAGTGGCCCTGGTCTGAACCAGGAGCCCTGGGGCTGGTCCCTGCCAGACAGCCCCTGTCTCTTTCTTTTTCTGCTGGGGACTTGGGGCATCTGAGCTTGTTCTTGTGGTGGATGGGGTCCTTGTGTGTGTTAACCTCTCCTGCCGGCCTTTAATCTGCATTCCTGGAAAACTGTGTTTCGTTCCTTCTGCGTGATCACCGTTCTTCGTGGTTTCTTTGTAG
Seq C2 exon
GTTCGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCCGAGCTTGGAGCCAAGGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGAGAAGAGGTGGATGATGAGAATCTGAGGGAGCTATTCAGCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:3
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTGTGATGAGAACGGCTC
R:
GCTGAATAGCTCCCTCAGATTCT
Band lengths:
247-1350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]