RnoINT0106599 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140993841-140994732:+
Coord C1 exon
chr5:140993841-140993937
Coord A exon
chr5:140993938-140994431
Coord C2 exon
chr5:140994432-140994732
Length
494 bp
Sequences
Splice sites
5' ss Seq
GAAGTATGT
5' ss Score
6.97
3' ss Seq
TTGGTGCTGCTCTCTTTCAGGAG
3' ss Score
10.26
Exon sequences
Seq C1 exon
GTGGATGAAGCTGTGGCAGTCCTGCAGGCTCATCATGCCAAGAAAGAAGCTGCCCAGAAGGTGGGCACTGTTGCTGCTGCTACCTCTTAAACCAGAA
Seq A exon
GTATGTTGACAGTTGACATTTTCTGCCTCTCTGGTGTTTCACATAGGGCCTTACTTAGCCTATGCCCCAGGATGATTCACTCAGCCTCCAGGATGCTGGGGGGCTACGTCCATGACTATGTCTGTAATCCCAGCTGTCCACGTTGGGGAGGCAGAGCCCTAGTACCCAGCTGCTCAGTCTGAGCAACCTAGAAGCACCTGATCACATGCTTGGCCACCACATAGAAATGAATAATCTCCTGGCCTGACATAGTGGCAGTCACATCATAAGACCTACCTGCATCTATGCATATCTTATACCTTGCTAGCTTGGCCTGAGGTGGGTGAGATTGTGTCCTGCCAAGCTGGGAGAGCAGTGTGCAGAGGGATATTGGTCTTGTAGGACTGGTACCTGAGAGGTGATGGACAGTTGAAGTCAGGGCGGGATGGGGCAGCTGATGCTGATGGAGTTCTTATAGCGGGCTGCTTATTTGTGTTGGTGCTGCTCTCTTTCAG
Seq C2 exon
GAGTCAAAAGCCAAATAACCCCTCACGGCATTCAGCTGAGGTCTGAAGACTTCCTAGTTTGTCTGTGGACCTCTTTCAAGAACCAAGTTACAAATTCAACAGGTCATTTTGTATCAAAAGGTCAATTATGAAGCACCTAGAATTTTTCAATTATAAGAATATATTCTCTGGGTTCTGTTGTGGCCCAGATGATGGTAACTTTTTTTTCTATTATGAGTTCTGTTTTTTTTCCCCTCTCCCAGAAATTGGTTTTGATGTACCCAAGACTTAAGTTTCTCAATAAAGGAAATAAAATCTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.621 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=23.3)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGAAGCTGTGGCAGTCCTG
R:
CCAATTTCTGGGAGAGGGGAA
Band lengths:
343-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]