MmuINT1026167 @ mm10
Intron Retention
Gene
ENSMUSG00000034732 | Pabpc5
Description
poly(A) binding protein, cytoplasmic 5 [Source:MGI Symbol;Acc:MGI:2136401]
Coordinates
chrX:119927196-119930165:+
Coord C1 exon
chrX:119927196-119927300
Coord A exon
chrX:119927301-119927836
Coord C2 exon
chrX:119927837-119930165
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:ENSMUST00000040961:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
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),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
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]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types