MmuINT0114467 @ mm9
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:122966202-122967581:+
Coord C1 exon
chr4:122966202-122966317
Coord A exon
chr4:122966318-122967441
Coord C2 exon
chr4:122967442-122967581
Length
1124 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
CTATCCGTGGTTTCTCGTAGGTT
3' ss Score
8.57
Exon sequences
Seq C1 exon
GTGGTCTGTGATGAGAACGGCTCTAAGGGCTATGCTTTTGTTCACTTCGAGACCCAAGAGGCCGCCGACAAGGCCATCGAGAAGATGAATGGCATGCTTCTCAATGACCGTAAAGT
Seq A exon
GTGAGTGTCCCAGTCTGGAGCAACAACCATCGCATGAGCCAGCCATGGCCCCACCTCGGTATTAACTGGCACACACAAGGCGGCTACTGGTTCTCTCGGCCCAAGTGTGGCCTGCTCCTACCTCTCCACTCCAGGGCTGGTGAGTCTCCCTGCCCGAGCCACGGCAGCCCTTTTGACTTGCCACAGTCGGCTCCCTGCCCGAGCCATGGCCTGCCTGCTGCCTCTCCCTTAAGGCATTCATCTGTGGGTTTTGTGAGCATCGGCAAGTGGGGCTGGCTAGGAGAGCGCTCTGAGCCCACTCTGAGCAGGGGTCTTGGCCAGCGGCAGAGTGGAGAGGCCCTGGGCTGACCAGGAGCTGGATATTGGCTACACAAACTCAGCTTTCTTTCCTTTGACTCATTGCTGCCCGTGGGGCTCTTGCTAGTTTTTGGCACCAAATTGTCCTCTAGTTCTTTTCCTCCGAACTGCAACAACATTTCACTGTCATCCATTTAATTGGCCTACGATGAAGTCCACCTCTTTCTGGGGACACTGCATGACGGTCTTGTCACTGCTGTGGGGTTGGGGGCAGAGCCATGTGGGAAAAGGCATTTTGCATTTTGGCTATTACAGGCAACAATCATTTCTGTTCTCTGGGGTGTAGAATAGACAAGACTGTGTTTTATGTCTGTGTCGGGTGTGCGGAAATAATTTCCTGTTAAGGTTACCAAGTGGTAGAGCGGGAGGGCAGAGGTCACCCGATTGCAGCTGCCTCACTGCTGGGCTAACCACTGTTAACAGTTTGGCTTGTGTCCTTCCAGAGGTTTTCTATGCATTTACATAGATGCACAGAAATGAACCGTTTTAAAAACATGGTCGTCAGGTTTCATCACGAAGGCAGTGTGATGTGGTAGGAGTGGCCCTGGTCGGAACCAGGAGCCCTGGGACTGGTCCTTGCAGGACAGCCCCTGCCTCTTCCTTTTTTTCTGCTGGGGACTTGGGGCATCTGAGCTTGTTCTCGTGGTGGACGGGGTCCTCGTGCGTTTTAACCTCTCCTGTCAGCCTTTAATCTGCATTCCTTTGGGCCCCCGGAAATCGTGTTCTGTTCCTCCTGAGTAACCGCCGCTATCCGTGGTTTCTCGTAG
Seq C2 exon
GTTCGTGGGTAGATTCAAGTCTCGCAAAGAGCGGGAAGCGGAGCTTGGAGCCAAGGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGAGAAGAGGTGGATGATGGGAATCTGAAAGAGCTCTTCAGCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257-Pabpc4:NM_148917:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTCTGTGATGAGAACGGC
R:
AACTGGCTGAAGAGCTCTTTCA
Band lengths:
254-1378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: