MmuINT0114469 @ mm9
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:122968114-122969113:+
Coord C1 exon
chr4:122968114-122968208
Coord A exon
chr4:122968209-122968975
Coord C2 exon
chr4:122968976-122969113
Length
767 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GATGTATATTTTCTCTCTAGGCT
3' ss Score
9.16
Exon sequences
Seq C1 exon
GTAAGACCCTAAGTGTCAAGGTGATGAGAGACTCCAGTGGGAAGTCCAAAGGCTTTGGCTTTGTAAGTTACGAGAAACACGAGGATGCCAATAAG
Seq A exon
GTGAGTGTACTGTGAGGGTTGGGAAGAGCCTGTGGGCTCTACCCATTGCATGGGAGAGCAGCTAGAGTGGTGGGTAGTGGAGTGGAGTGGTGGGTGTGCAGCATCAGCACTAATGCTGGGCCACAGTTAATGTATCTGCAAACTCGTGTCACCTCGGATACTGTTGGACGATTGGGACAGATGGTTGTTCCATTCTTGGATAGGGAAACTGAATCCTATTGACTAGGTAGGGCAGTGTGCTGGACCCTTACCCTACTTACAGAGGGACCTGAAACATTGAGCATTGCCAGATCATCAGGCCCTTGCCTATAAAATTTATGCAAATACTGGGTTTTGGGGGCCACCACTACCCCCATCCCACCACCCCAAGCGCCCTCTGCACTAAATCTTTCCCAGGCCTGCTGCTTGGTGCCGGTCTGGGGACAGACAGTGCTATACTACAGCAGAGGAAATCCAGACGGGTCGTTTCCATCTGCCCTGGGGCCTGTCTCTACAACTCTGCCACACTCCCTGAGAATGGAGACAATTTTGAAGATGCTGAAGCTAGGGGTGGGAACTAAGAGCAGAAGATGTGTCTGGGCCAGTAACTCCGATGCTAACTCCACTTCCCACGGGAGTGTAGCAGGCTTCAGAGGTCCGACAACGCTGATTATCAGTCCAGCGGGGAAAATGGTTTTTTTCTTGGTGTTCTGGACTCTGCTCCAGAAGACGACCATGTCTCTCTGCATTATACATGTCTTCATTAAAGATGTATATTTTCTCTCTAG
Seq C2 exon
GCTGTGGAAGAAATGAATGGAAAGGAAATGAGCGGGAAAGCCATATTTGTAGGCCGTGCACAGAAAAAGGTAGAAAGGCAGGCTGAGCTGAAGCGGAAGTTTGAGCAGCTCAAGCAGGAGAGGATTAGCCGGTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257-Pabpc4:NM_148917:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.109
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGACCCTAAGTGTCAAGGTGA
R:
TGGTACCGGCTAATCCTCTCC
Band lengths:
230-997
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: