MmuINT0114474 @ mm10
Intron Retention
Gene
ENSMUSG00000090919 | Pabpc4l
Description
poly(A) binding protein, cytoplasmic 4-like [Source:MGI Symbol;Acc:MGI:3643087]
Coordinates
chr3:46442197-46448219:-
Coord C1 exon
chr3:46448061-46448219
Coord A exon
chr3:46447290-46448060
Coord C2 exon
chr3:46442197-46447289
Length
771 bp
Sequences
Splice sites
5' ss Seq
CCGGTGGGT
5' ss Score
7.85
3' ss Seq
CTGCGCTTCCCCTCTTGCAGGAA
3' ss Score
11.64
Exon sequences
Seq C1 exon
TGAGGCTCGAGTTTCCTGGGAGGAGGGAATGCAGATTCTGCAGAAAGTTGCTGGGCTAGCTATACGGTCCGGACCTGGTCAAGGCCATCACAGGTTGTTTCCAGGACTTCCAGGATCCCGATCTTTGCTTGGGAGGGCTGGCGTGGACAAAACAGACCG
Seq A exon
GTGGGTGTGGGTGTGGGGGTGCGCGCGCGCGGGGGGGAGCAGTCTGGTGGTGGGTTTCCCGGCCACACCCCCAGACGTTTTCTCCACCCATGACACCGCCTCTTTCCCTGAGCCCAGCTGCAGAGGCTGGGGAGCGAGCCAGAGGGGCGGGGGAGGAGCATGGTACCCCCCCAAAAAAGTGTGAAAGAGCAAACAGTGCTAGCCAGCGAGCTCCGGGTTCCTGCCGCCTGCAGTCCATAACCTGGTGAGCTTCAGTTTTCAGCCAGGATCGTCCCGGGCGCCTCTGGCCACCGGGGTGGGGGGTGGGGGGTGAGGGACGCGGCCCAGGCGGGCTCTCAGCCGCAGGGCGGGCGGCGTGGGTCGGGCTTCCTGCGCGGGACAGACGGGGGCCTGGGTTGCACGCCCCCCTCTGCCTTGCTCTCCCCAGGCTTGGCTGAAAGTTTAAGCCAGCAGAACACAGGAACACAGCACAGGGTCTGGGCCTGTTTGTGCTCCGAAACCAGCCACCAGCGCCTGGGATGGAGGCAGATGAAGGGCCTGTCCTGGCCAGCCACTTGTAAGTTGTTGCTGAGTTGGAAGGGAAGGAAAGCTGAGAGGTGAAGGCAGATTGCCAACTACCAGGAGAGGACATGGGTTTCTGGCTTTTTTTTTTTTTTTCTTTTGACTAGGTATTGCCTGGAAAGTGCAAGTGACCCTGTAGCTGGACCTCTAAGTGGTCTTTGGAGGCCACTGTGCAGGTCCTGAGTTTTGACTGCGCTTCCCCTCTTGCAG
Seq C2 exon
GAAGCTACAGCCTTGAGAGCTGCAGGCTTGTAGAGTTGGGGTCAAAAAAAGGAAATAAACCAAACAAGCCAAGAAGAAAAAGATGAGTCTGGAAGCTAAGTACCGTGCAGCTTCCCTCTACGTGGGTGACCTCCACGAAGATGTCACGGAGGACATGCTCTTCAGGAAGTTCAGCACAGTGGGGCCGGTGTTGTCCATCCGAATCTGCAGGGACCTGATTTCCCAACGTTCACTAGGCTACGCCTATGTCAATTTTCTCCAGGTTAATGATGCCCAGAAGGCCTTAGTCACCATGAACTTTGACGTGATCAAAGGTAAATCCATTCGTCTCATGTGGTCTCAACGGGATGCTTGCCTGAGGAGATCGGGAGTCGGGAATGTGTTTATCAAGAATCTGGACAAATCCATTGATAACAAAACCTTGTATGAACACTTCTCACCTTTTGGAACGATCATGTCTTCCAAGGTGATGACTGATGGAGAAGGCTCCAAGGGCTATGGCTTCGTGCACTACCAGGACCGGAGAGCGGCAGACAGGGCCATTGAGGAGATGAATGGCAAGCTGCTGAGGGAGAGCACTTTGTTCGTGGCCAGATTCAAAAGCCGTAAGGATCGGGAGGCTGAGCTCAGAGACAAACCAACCGAGTTCACTAATGTGTATATCAAAAACTTTGGAGATGACGTAGATGATGAGAAGCTCAGGGAAGTTTTCAGCAAATATGGCCAAACTTTGAGTGTTAAGGTGATGAAAGATGCCACTGGGAAGTCCAAAGGCTTTGGATTTGTGAGTTTTGATAGCCACGAGGCTGCGAAAAACGCAGTTGAAGACATGAATGGACAGGACATAAACGGGCAGACGATTTTTGTAGGCAGAGCCCAGAAGAAGGTAGAACGACAGGCTGAGTTAAAGGAAATGTTTGAGCAGATGAAAAAGGAAAGAATCCGTGCACGCCAGGCAGCTAAGCTCTACATTAAGAACCTGGATGACACCATCGATGATGAAACACTGCGCAAGGAATTTTCAGTCTTTGGGTCCATTTGCAGGGTTAAAGTGATGCAGGAAGCAGGGCAGAGCAAAGGCTTTGGCTTAATCTGCTTCTTCTCCCCGGAGGCAGCGGCGAAAGCAATGGCTGAGATGAACGGCCGCATCCTTGGCTCCAAACCCCTCAACATTGCACTGGGACAGAAGCACTGAGCCCAACATGATCCTACCTCGCAATCTGAGAAGCAGCTAGGAGAACGATACTGCTCTCCATCTTTCCGGTGCTATAAGGAAGGGTAATCTTGAAAAAACCCAGTGGCTGCTTAATTTACTGCAATCGTGCAAGGAAATGTCTATACGAAAACATTTCGTTTTATGTGAATGAAAAAAAAATGTACGTTAGAAGTTTGATTTGTTTTACAGAGCATATCTTCAAAAAAATTTAAAAATTCTTATTTTCTACTACTTAGAACCGTTTAGTTGGTTACATTCATATTACATTTTGAATTAAGTGAACCAAATGCTTGTCTCTATTGAATATTTTATTCTTTCAGGTTAATAACTGTGAGCTTTAATTTCTCCTATAAAAATTGCCCATAACAAATTTAATTTTTTTAAACTAACAAGAATCTTTTAACTTTTTTTTTTTTTTTTTTTTTTTTGCAATTCAAAATGTAGAAATTGGTAGCCAGAATGAAGTTAAATCACATATTGCACTTCTGAGTTAATCCATCCAAGCCAAAGTTCTAATATACATGCATAAACATATTCTGGTGTATTTGGTTTTATTCTATTTTAAGATGATGTTAGAGCTTTCTGGGGTTTGGTTTGGTTTGGTTCTTACACTTTTTGTATATTTGCTGTAATCTGCTTGGTGTTTTTTTTTTCTGCTTCCTTATGTTATATACATTTATCTATGCTGTTTATGGACATTTAACTTCATCTTAAATCAAATCACACCCATGTGGTTCAATGTGATGCAATTTTAGGCATTCACTAGATGCTGATGTTGTGAAAGTCATAGCTATGCAACTCAGAAACTCCATCTAATGTAAATCTTGAAAAAAATCTTCATGTTATAAAAATCTATCCTGGTTTTCAGAATATAAGTGCCTTATTTTTCTAAATCTCCACCTCCTTTTATTAGACTGTGTTAGCCCTGTATTAGACTGTGTTGCGTTTGCGTTTGCTCTTGGCCTTGGCTCATGTTCCGACAAATGTGAGGTTATGTTGCTTGATGTGTGTTTTAGCATGTGTTTTATTTGACACTCTTCCCACATGATGTATCTATTCTGTCCATAAAGTCTAACTCATTTTTACACATTTTTACAAAGACACTGTCATATTGGTGTTTCATATAGGCTACCTCAAATCTATCTGAAATAAGAGGTAAGAGTTATTTATTTACAACTTACTCATTATCTTAAAAATGTTACCAAAGGTTGGAAAACTCATGTTATTTCTTCTGCTTTCCATTCTTTCTGGTTCTTTCATTCTTCTCCATTTTTGATTGTTTGGTCATTTCTTATTACAATCTTTTAATTTATGTATTACAAATACATTTTTTCCTTAACAAAATTTTATGAGGAAAGTTTCATTTTGTGTTTATAAACCATATATACATATATACGTAGCAAGTTTTTCTAATCTCAATGAGAAAAGAAAACAGTTTAAAAAAAAGTAAAAAAAAAATATTTTCTACAAATACATTCTGCTGAAATCTGCCACATATTGTCCCTAACTTTTTATGTGTACACTAAGAGCTGATTTAGGAAAGGCGACATCAACAATTTTGTTTGAAATCATTGTTTTGTATTTGATGTTGTCAGATGCTCAAACGTAACTTACTCAAGGAATGACTTACCTATTACATTAGGGGCTTTTGACTTTGGCCAATGGGTTTTCCATGATTCCCAAACTCTTGAGAAATATGGGTGGCTTTGCAATGCTTCTCTTCTGGTCTTGACTTCTGCCAAGATAACTTGAAGGTACGCATTCTTCCCAACTCCTATTGATATGCTTCCAATTCTTTTCTGGAAAAATAAACTATAATTCAGGACTTAAAATCAATTTATTTTCATGTGTTGCCAAAATATCTTACAGATATTTCATAACAATAACATTTTCATTGTAAGTATAGGCAAATGCACATTTCCATATTGTCCAAGGACATAAATATTTTGTTAGGATCTGGCAGATTGAGCATAGTTATGATAAATAACCACTACTCTTTCATTGTATGGTTTTAATAGCTTCTTTTTTTTTAATTGTCAAATTTTTACCTGTGTCCATTGCATTAATATTTCAACACTTGTAAATTTAGTGTTTCAAGAACCTAAGCTATTTTTTCTCTTGAGTATTTATATCCACAGTTTTCTATCACATCAAAAACTATTTTAAACCTTACCAATGTTCTCACTTTGTTTACAGTTTGTAAAGCTGTCCCAAAGACAGATTTTGAACACAACTTTTTCAGTATCTCATTGAGATGACATTTTTTATTGTGATTTGTTCTAAACACTTTAAAATGTCTGTATATACACATGTAGATGTACATGTGTGTGGAGTATAAACATGGAGACAGGTAGGCAATCCATGTTGTCTTCTATTAATGTGTATGGCTCATATTATCAATATTTTTATAAACAAAACTTGTTTATATTTTGTGTAAAGAGTACAATAAAAGTTTTAGCTATGTCTTGCCTCTACACCATTAAGCAGCACATGTTTGGGTTAGTACTGATATAAACTGTATCAGAGCTGATATATACACTCAAATTCATTGGCTTGCAGAATCTCTACCTTGATGAGTATTTTCATCATCAGAAGTACCAGAAGTTGCCAGGACTGGAGAGTACAAAATGAAAACATTTTCTGGGAGATTTAATCTGCAAAAGTGTCCAGATAATTGAACAATGAAAACATCTCTCTTTTGTGCACAAATAATTGGTTAAATAGTTTACCATATGCATAGATATATTGTTATATCAGCTTAATAATGCAGTATCCTAATACCTTAGTAGAAATTGTATATTCCTAGTATTTAGCATAAAATTTGACAGTTCATTCTCTTTAATTTTTAAATATTATTCATTCTAAATTTGTGTGTATGTTTGTGCACATGTGTGAATTTGTGCATGCATCTGCATGTGTGTGTGTGTGCATGTGTGTTTCAACAATTACATTGTATCTTCCTAGTTAACAAGTTTTCACAAATTAAAAATTTCTGTAACTAAGTGCCTTGAATAAGAAAGACAATCTTTGCTTCATTAATAAATCAAAGCTAATCCAAACAGAAATGCCTTCAGCCAGTATCTCTACTCCTCCCCCACGTATACTCCCTATCTGTTGTATAGATGACTATGTTTTACAGATGATGTAACACATATGTGCCTTGTTCCAGTTTTCAAAAGTCACATGGAAATTGTTAAAATATAATTTAATGTTCTCTATATTCTTCAAATCCTAAAGAGACAATACTAAACATAATTTACCCCGTCAATGATGGATATGTCTGCGTTATTTATGTTCATTTCAATTATCTGTTTCTAAGTGTAGGTGTTTATATTTCATGCTTTTAAATGTTTCATAATTCTTTGACCTGAAATCTGGTTCTGTACGTATTCACAATAAAAGGATCAGTTATTCAGTAGCTGTTCTAACGTGTAGCCAGGTTTCATAAGAAACAGTTGACTGTTGTGTTAGTTCAGACAGTACTCAACGTGTGAAATCATTTAAAAAAATGTGAAAAAATGCATGATGCCTTATAAATCAAAGTTTGACAGGCCAATATTTGGGATGGCTTTCTTACGAACAGACACTAAGAATGATCATACCATCACTAGATGAGAGGGAACCTTAATGTGTGCTCGCTCTGTTCCTTTTCTTCTTCCCCTTCCCATTCAATAGCCTCCAACCTTTTACCTTGGAGGCTCCACTTGAGGGAGCTTGTCTACTCTTTATCATCACCCAAAGGCATGCTGTTCACAGCCAACCTGAGATAAGATTGGCATTCTAGGTGCCTTAAGATGGGGAATAACTTCCTCACATATGTGCTTGAGTGACTGCCTGCATGTGAAAACTATAGCAATTAAAAACATAAAATTCATCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000090919:ENSMUST00000192793:1
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=19.1),PF0007617=RRM_1=WD(100=18.6),PF0007617=RRM_1=WD(100=18.9),PF0172511=Ham1p_like=WD(100=29.9),PF0007617=RRM_1=WD(100=18.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
TGGGAGGAGGGAATGCAGATT
R:
GATTCGGATGGACAACACCGG
Band lengths:
348-1119
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