MmuINT0114457 @ mm9
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:163862847-163868301:+
Coord C1 exon
chr2:163862847-163862942
Coord A exon
chr2:163862943-163868052
Coord C2 exon
chr2:163868053-163868301
Length
5110 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TTGTCTCCTCTTGCTTTCAGGTG
3' ss Score
11.85
Exon sequences
Seq C1 exon
GGTGTGAACCTTTATGTGAAGAACCTGGACGACTCCATTAATGATGAGAGGCTGAAGGAAGTTTTCTCTACCTATGGCGTGATCACCAGCGCTAAG
Seq A exon
GTGAGAGGTGCCGCTCTCCTTGCCTTCATGCATCCCCCACCCTCTCAGCTTCTCACCCCTGCACAACCCCCAGCTTCTCACCCCTACACAACCCCCAGCTTCTCACCCCTACACATCCCCAGATTCTCATCCCTACACATCCCCAGATTCTCATCCCTACATACCCCAGGTTCTTAACCCTGTACACTCCCAGCCTCTCACCCCTGCATAGCCCAAGCCTCTCCGTTAGCTTCCAGAGACTTTGGGTTAGGTCCCTCTTTCTGTTTCTGGCTAACACCTTTGGAGGTCTATTGGCAGCCTTATCTGGACTGGATGGGGGAAAAATAAACATATAATGTAGGCATCGCATTGGGCTTGAAGTACCGCAGTTTTATTTTATTCAATAATTGCCCACAGATACCTACTATATGCCAGATTCCAGAAATGTATCCTCTGTCTGGACCTCAGTTTACTCATTTGGAAAATGGGACACCTTCATTCTATATTCCCCATTTGTTGAGTACCAGTTGTGTGCCCAATCTTGTGACATACCTAAGATGTGACAAATGGCCATCCTCTCCAGCAGTTCCATGACTGTGAAGGAGGCTTAGGGTCCACGTCTCTCTCATAAGATGAAAGTACAGCACGAGCTGCATGGGCCTCAGCCCTGGCTTCTCATCTGGGTCAGACAGGCTGCATGTGGAGTTCTGAGGGCATGACCTGAACATTTGAGTTTTTATTTTAATTAAAGTTGTATTACATCTTGTTGTGTATGTGTGTACACACACACACCCAGAGCTCAGAGGTCAACCTGTGGGGGCTCAGTTCCCTCTTTCCACTGTATGGGTCCCTAGAGGTCTGACTTAAGTCATTGGGCTTGGTAACAGGTGCCTTTACCTGCTAAGCCCTCTCTCCTGCCCCAGGGATATTTGACTTTATAAAGTAGCCCAGGTGGTTGTAAAATGGCCCAAGATTTATTCATCTCATACCAGGGTCTGTGGGAAGCATATGCAAATGAGTAAGACACAGTCCATGCCTTTGAGGGCTTTATGATCTAGTGATAAGGTCAGATCCATCACTACCGTGAGATGAGAAGTCGGGACTTGGGAGAGCTCAGTTGGTAATGTGCTTGCCTTGCTAGCATGAGGACCTGATTTCTAGCCTAAGAACGTGGGTAAAACTAAAAGTCAAGTCTGGTGGTGTGTGCTGTGTGAAGTGTGTGGTGGTGTATGAGGCAGTGAAGTGCTGTGTACTGTGTGTGGTGTGGTGTAGTGCCATGTGCAATAGTGCAGTATTGTGTGCAGTGGTGCACTGCTGTGTACTGTGTGTGGCGCTGTGTGCAGTGGTGCAGTGCTGTGTACTGTGTGTGGTGCTGTGTGCAGTGTTGTAGTGCTATGTGCAGTAGTGCAGTGATGTATGCACTGGTGTGGGACTGTATGCTGTGGTGCAATGCTGTGTGCAGTGGTGCAGCACTATTGCAGTGCTGTGTGCAGTGGTGTGGTGCTATATGCAGTGGTACAGTGCTGTGTGCAGTGGTGCAGTACTGTGTGCTATATGTGGTACTGTATGCAGTGTTGCAATGTTGTGTGTGTTGTAGTGCTGTGTGCAGTAGTGCAGTAATGTATGCACTGATGTGGTACTGTGTGTGCAGTGGTGCAGTGTTGTAGTGCTGTGTGCAGTACTGTGGAGCTGTGTGCAGTGCAGTGTGCAGTGGTATGTGTGGTGCTGTGTACTGTATGCAGTGGTACAGTGCTGTGTACTGTAATTCCAGACAAGCAGATTCCTGGGGCTTGTCTGCTATTCAGTCTTTTCTACTTGAGACCCTGTCACAAAACAAAGGTAGTTGCTACTTGAAGAATGATACCCATGGTTGTCCTCTGGTATCTGTAAACACATGTATGTTAACCTGCAGACATGAGCATGTGTCCTGCACATTAGCACATGCACACACATGAACATGCACATTAGCATTTGCACACATATACACACACAGAGGATGGGAGGCAGTGTTGGATACAGAGATGCAGGAGCTTGGTGGAGCAGTTGGGGGCTTCGTGGAGCAAAAGGAAATGGCCTTTGACTTGGCAATGACGAGATAGGGAACAGAAGTAGGAGTGGGTTATACGACGAGGATTTATCTAATTATATACTTTTTCTATTTTATACAAAATGTGATAAAAAATTAAGTCAATGAGAGAAGAATAAATCAAAAGAAAGCTTAAGTGAATGAAAGTGTATATACTGTCTATTGTAAATGAGCCATTGCCAAGTTAACTGTAAATTCCACTTACATTTTAGTTTTAACAAAGTTATTGTTCTCTTTTATAATTTGTTTGTTTGTTTATTTTGTTTTGTTTTGTTTTTTTTGAGACAGGGTTTCTCTGTGCAGTCTTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGACCATGAACTCTTAGAGATCCACCTGGCAGACAGATAATTTTTAAAAAGGGAACAATAAAGTCAGGCAGTGCATCAGCACTCAGGAGGCAGAGGCCTGTGCATCTCTGAGTTTGAAGCCAATCTGGTCTAGAGAGTGAGTTCTAGGTCAGCCAGGGCTACACAGAGAAACCCTGTTTCAAAAAATCAAAAACAAAACAAAAAAACTATCTGCTAACAGAAACCCTTTTTTTTTTAATTTTTAGAATTTTTTTTATTCTTCGAGATAGGATTTCTCTGTGTAGCCCTGGCTGTCCTGGAATTCACTCTGTAGACCAGGCTGGCCTCGAATTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGTCACCTCGTCCAGCTAACAGAAACTCTTAACAATATCTCTTCATGGAGACCTCTGGTGTCTGGGTTGGAGATGATGCAGTGGGTAAGAGTGCTTGCTGTACAAGCATGAAGACCAGAGTTCAAGTCCTCATAACCTACATAAAAACTTAACTCTTCTCATGTGTGAGCTTGTAACCCCAGTGCTATGTTGGATAAAGACAGGAAGATGGCAGAGCCTGTTGGCTGCCAGCCACAGTGAGACTGTCTTCAGGAAATAAAGTAGAGGGTGATAGAGAAGGATGTCTGACATCCTTCTTTGGCCTCAGTGTGTGCACACACACACACATCAGACACATATACACACACTCACATATACACATATCATACACATATACACACACCACATATATACACATCACACACATACACACACATATACCACATATCACACACATACACACATCAGACACATACACCCACACTCACACATATACACATCACACACACACCACATAAATATATACACATCACGTACATACAACACACACATACACATATCATACACATACACACACTCACACATACACACATCACACACATATCACATACATATACACACATCACACACACACACATCCCACATATGCACACTCTCACACATGCACACATCACACACATACATACACATGCAGCACATATCACACACATCACACACACATGTACACATCACACACATACACACACACTCACACATACATCACACACATACACACACACACACCACACACATATACATCACAAATACACACACAGAGCACACAGCACACACACACACATCTCACACACACAATGACATCTAGTGTGATGAGTTTATGTGTGATGTGCGTGTATGTATGTGTAGTATGTGTGTGTGATGTGTATATGTGTGAGTGTGTCTAAGAATATTTTTAAATGCAAAAAAAATAAAATTCATAGAATCATCAGGAAGCCAGTTGTGTCAAAATCCAATTACCAAACTACGATAGCAACAGGCCTGTGTGCTGTGTTGTTAATGTGGTCAAGCCAAGGATCATCATGATAGCAACATGGATAGACAGCACGTGGTGATCACCATCAGGGTGACATCAAAAGATTTGATTTCACAAGCAAGCCACAGGCGTGGCCCACGCCGCTGTGCTTTTTCCTCTTGGCTGCTCATTTCTGTAACTGCGGTAAATGAAGACACTTTTGCACAATTCCATCTATGCCCCTCCCTTCAGGCCTGCAATCCAGGGGTGTGGCAGTTTGAGAGTCACTGCTGGAGTGGTGCTTTAAAGGGCTCTTGCCTCTCAGGCCTGAAAAGGGTTAAGAATGTCCTCTGCATCTTGTCTGTGGAAAGATGAGACTGGTTAGTTCAGAAGCTCTGATCCCAGCAGCCATGACAGGAACTAGCAGTTGCACAGTCGACAGACAGCCGTGAGGGAACTCTGAGGGAACTCTGGGTCTGAGACATACAACAATCTCTCTCTCTCTCTCTCTCCCTTTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCCTAGATAGCACAGGCTGGCTTTGACTCACTATGTGGCACAGGCTGGCTTTGAACTCACTATGTAGTGCAGGCTGACTTTGGGCTCACTGTGTAGCGCAGGCTGGCTTTGAACTCTCAATGATCCTCTTGCCTTGGCCTCCCCAGTGCTGGAGTAACAGGTGTGCACCACCACACATTGTTCTCTGTAATGCTCTTTAAGCTTTTCTGGGAGTCTAAAGTGATAAAGTCTAAAGTCCACATTTATAAGATAAGAAGGCAGCAGGTGGCCTTGGACGAGTCACTCTTTTTTTTTTTTTTAAGATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTTAGACACTCCAGAAGAGGGGGTCAGATCTTGTTACAGATGGTTGTGAGCCACCATGTGGTTCTGGGATTTGAACTCCGGACCTTCAGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCTGGATGAGTCGCTCTTGAGTCACCATTTTCCCATGTAAAGGGGAAGCCATGGTTCCTCCTTCATCAGGAGGCCTACTGTGTGCCACAAAGGCTCATGAAGTGTGTGACACACAGTAGGCCTGAGTAAATGAGGGGGTGTATGGTTTGCCCATTATCACAGTCTGCCTCAGGGTCTGCTGAGTGGTGGATGTGGTCACAAAGGAGAAGCATGTATCCCAGGAGTCTTGCTTCCCTGTGCCCAGCAACCCTTGTCTCCTCTTGCTTTCAG
Seq C2 exon
GTGATGACAGAAAGTAGCCACAGCAAGGGCTTTGGCTTTGTGTGCTTTTCCTCTCCAGAAGAGGCAACGAAGGCCGTGACGGAGATGAACGGGCGCATCGTGGGCACGAAACCGCTCTATGTGGCCCTGGCACAGCGCAAGGAGGAGCGGAAGGCCATCTTGACCAACCAGTATAGGCGACGCCCCTCTCACCCTGTCTTGAGCTCCTTCCAGCAGCCTACCAGCTACCTGCTCCCTGCTGTACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582-Pabpc1l:NM_001114079:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=47.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: