MmuINT0114475 @ mm9
Intron Retention
Gene
ENSMUSG00000034732 | Pabpc5
Description
poly(A) binding protein, cytoplasmic 5 [Source:MGI Symbol;Acc:MGI:2136401]
Coordinates
chrX:117040805-117043774:+
Coord C1 exon
chrX:117040805-117040909
Coord A exon
chrX:117040910-117041445
Coord C2 exon
chrX:117041446-117043774
Length
536 bp
Sequences
Splice sites
5' ss Seq
TCGGTCCGT
5' ss Score
3.06
3' ss Seq
TCTGAACTTCATTTTCTCAGCCT
3' ss Score
3.93
Exon sequences
Seq C1 exon
AAACCAGCCTCGCGTCAGAGCTGAGCACAGCGGCGCGGCTGCCAGTCAGTCCCTCCGGACCTGCGGAGAGAGCCTCAGGCTGCAGAAATCACCGCGCCTCACTCG
Seq A exon
GTCCGTACCCAGTGGTCATCTTGGGGATATGGGCGGTCTCCCGTTCCCTACGCATGTTTCTGTGTGTCTGTCTCTCTGTGTGATCGGCTGCCAGCAGCCTGCCTGCCAGTTCCAGTGCACCAAGTGTTTTGTGTGCCCTTTAGCTGATGCTGAATGCAGAGAGGCCTTAGTGTGCTGCAAGCCCTCCTGACATAGGCAGGCGGAGGAATACACACTTGGTCCCTTGCTCTGGGTGGCTGACATGTTTAAACCCACAGGAGCTCAAGGCCTATGATTTTGCAGAAAGCCAGTCACAAGGCCTCTGTTGGTGAAGCTAGATGTGGGGAACCAGTCAGACCCTTGGTGATATCTTTAATTATAAAGGGGTAGGGAATATTGCATTTGTAATACAGGCTTTTGAAACTGATTTTAAATCTGAAGGGGTAAAAATCTGTAAGTCTTCTTATGGAGAACAGATTGCTTATTGGGTTGCCTTTTTGTCTGATGTATTTGTTCTGAGCCTGCTGACCAGCTGTTTCTGAACTTCATTTTCTCAG
Seq C2 exon
CCTCAGCCTCAACAGTGATCTGAGTCTGCTTTTAGCTTCCCTTCACCTGCCTTGGCTTGTTTCTGTTCAAGAACAGCTGTTTGGCCTATAGATTAGAAAAAGTGCACCCCCTCCCTACTCTGTCCCAAGAGATCATCTTCTAAGTGCTCAGAGATGAGTGGGGAGCCTAATACTGCTGGCAAGAAAAAGAAGTACCTCAAGGCTGCCCTGTATGTAGGTGACTTGGACCCTGACGTCACAGAGGACATGCTCTATAAGAAGTTCAGACCTGCTGGCCCTCTGCGCTTCACTAGAATCTGTCGTGACCCAGTGACCCGCAGCCCCCTGGGTTATGGTTATGTTAATTTCCGCTTTCCTGCAGATGCTGAATGGGCATTGAACACAATGAATTTTGATTTAATTAATGGTAAACCATTTCGCCTCATGTGGTCACAGCCAGATGACCGTTTAAGAAAGTCTGGAGTTGGAAATATATTCATCAAAAACTTGGATAAGACCATAGACAATAGGGCCTTATTTTATTTATTTTCGGCTTTTGGGAACATTCTTTCCTGTAAAGTCGTATGTGATGACAATGGCTCTAAGGGTTATGCTTATGTCCACTTCGATAGCCTTGCTGCTGCCAATAGGGCTATCTGGCACATGAATGGAGTGCGGCTCAATAACCGCCAGGTATATGTTGGTCGATTCAAATTTCCTGAAGAGAGAGCAGCAGAAGTCAGAACCAGAGAAAGAGCAACATTTACCAATGTTTTCGTAAAAAACTTTGGAGATGACATTGATGATGAAAAACTAAACAAACTTTTCAGTGAATATGGGCCAACTGAGAGTGTTAAAGTCATAAGAGATGCCACTGGGAAATCTAAAGGCTTTGGATTTGTAAGATATGAAACACATGAAGCTGCCCAAAAGGCTGTGCTAGAACTGCATGGCAAGTCAATAGATGGGAAAGTCCTATGTGTAGGGAGAGCACAGAAGAAAATTGAACGCCTGGCTGAATTAAGGCGGAGATTTGAACGGCTGAAATTAAAAGAAAAAAATAGGCCTTCAGGAGTGCCTATCTATATTAAGAACTTGGATGAGACCATCAATGATGAGAAACTAAAGGAGGAATTTTCTTCATTTGGATCAATCAGTCGAGCCAAAGTGATGATGGAAGTGGGACAAGGAAAAGGGTTTGGTGTTGTCTGCTTTTCTTCTTTTGAAGAGGCGTGCAAAGCAGTGGATGAAATGAATGGTCGCATAATAGGCTCCAAGACATTGCATGTCACTCTGGGGCAAGCTAGGCACAGGTGGTGAAAATTACTATGAGCAATTTGTTTAGCCTTAGCCAGTGCCTACATAGCTTGGGCTCCTTTGTGACAGAGGTTATTTTCTCTCAATTCATAGGTTTGTTTTCTTTCTTTTTATTTTATTTATTTATTTTATGACACTTTCTTTTGGAAACAAAGTATACATAGAAAATCTTGTTCATTTTGGTGACAAACATAATTTATAAATGTAAAATGTCATTTTGTACAATTTTTATAAGATCTTTATCCTTAGAATAAAATTTATCATCTTTATTTTTTCTAAGTATCCTGAATGAGGAAAATGATTATATTTTCTTTATTTTCATAATACTAACTTAATTTCTTCTATGAAAATATTCTTAAGAGATTCCTTATTTCTGATTCTGGCACAGTGAAAAGTCAACCGTTGCTTTTTAAAGAAAAAGTGAATGGATAGGGGCCACTTAAAATTTCTCCATAATTTCATTTTAAATTATGATTTAAATTGAATAGTACTTAAAACATATGAGGCATTTTTCCTTTATTTTTTGTATCTGTTTTTCTTGTATCAAGTGCACACTACAGATTTGTTAGCAACTTTGACCAGTTATTGGGATTTATCTTTATAAATATCACGTTATTGTTTCTTAATCAGTACTTCTAAAAAAACTGTTGCATTGATAAATATCTATTTAAAATGTGAGGGTCTCAAAAATATTTGCCAAGAGATATATTTGAAGATACTCTAAAAGTAATTCTTAACACTTGTTTTCAAAATGTGTATAATGCATAGAGGTAGACTATGCTAAATTAACAGAAACATTTATTAGTGTACTAACTCACTTTTACCTTTAAACACCTTATACACTGCTGCTGTAAAACTAAAACATGTTGTTTCTTGTCATGTTTGAATATATCCACTGGCAAACACTGACATGTGTTTTATTAAGGAATATGTTTTCCCTTATTTAGGTCATACCTTTTCATCCATTATGTGAGAATCATCAACTCCAAATAATTCTTTACTAATTCAGACTACTTAAAATATGCTGATTCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034732-Pabpc5:NM_053114:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0007617=RRM_1=WD(100=18.6),PF150631=TC1=WD(100=12.6),PF0007617=RRM_1=WD(100=18.1),PF0007617=RRM_1=WD(100=18.1),PF0007617=RRM_1=WD(100=18.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAGGCTGCAGAAATCACC
R:
GGTCACTGGGTCACGACAGAT
Band lengths:
348-884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: