MmuINT0114433 @ mm9
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36535499-36538728:-
Coord C1 exon
chr15:36538069-36538728
Coord A exon
chr15:36535693-36538068
Coord C2 exon
chr15:36535499-36535692
Length
2376 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TGAAAATGTGTCTCTTGTAGCGG
3' ss Score
8.47
Exon sequences
Seq C1 exon
CCCCTTCTCCCCGGCGGTTAGTGCTGAGAGTGCGGAGTGTGTGCTCCGGGCTCGGAACACACATTTATTATTAAAAAATCCAAAAAAAATCTAAAAAATCCTTTGAAAAAACCCAAAAAAAATTTACAAAAAAATCCGCGTCTCCCCCGCCGGAGACTTTTATTTTTTTTCTTCCTCTTTTATAAAATAACCCGGTGAAGCAGCCGAGACCGACCCGCCCGCCCGCGGCCCCGCAGCTCCAAGCAGGAACCCAGAGACCGAGGCCTTCCTGCCGCCCGGACCCAGCACCGCCAGCCTCGCTCCCCCGGTTCCACGGCCGTTGAGTACGCGTCGATTCCGGTTGAATTTTGTCCCTCTGCGCTCGCCCCCGCTCCCCTCCCCCCGGCTCCGTCCCCCGGCCCCGCACTCGCTCTCCTCCTCTCACGGGAAAGGTCGCGGCCTGCGGCCCCGCGGGCAGCCGTGCCGAGATGAACCCCAGCGCCCCCAGCTACCCCATGGCCTCTCTGTACGTGGGGGACCTGCACCCCGACGTGACCGAGGCGATGCTCTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCCGCTCCTTGGGCTACGCGTACGTGAACTTCCAGCAGCCGGCGGACG
Seq A exon
GTGAGCGGCAGGCCGGAGGGTGGCGGGCGGGCGGCCATGCGGCCGGGGCGGCGGGCCTAGCGGGGCGGGCGAGGGGGCGGGAGGGCACGGCGCCGCAGCCCCTCGCGGGCCGGCACTTCCTCCTCTGCGACCATTTTCTCGCCATCGGTCGCTCTCAAACTTTAGGGCGATGACGCGCCCGGAGGGTGGTTGAGATAGCCTTCACCGCGCTCCCGCCACAAGCTGTGGGATTCGGGGGTTTCGAGTACCCTCCTGGAGCGGCGGGTGGAGGTACCCCTCCATCCCCTGCCCTGGCCCGGCAGTCAGGCCGGGGAGGAAGTACGATTCAGTGTTGGGAAATACCACGTGTTGAACCCTGTAACCTCACAGGCCCGAGGCCTGTTCCTGCCGGTGGCTCAATCGCTGGGAGGAGCCCTAGGCTTTAGAAGAAAGTTAAATAGGGTGATGCCTGGTGGTGGTGGTCCTTAGGGTCGTAAGCTCGTTCCTAATAGCACATCTCTGACCTGTGGACCAGGAAAGGCACCTTATACCATATATAATTGCTTGGGGTTTTCCCTAGATGAAGTATTCTTTAACCATGCCGTGGAGGAGGGGATGTGGAAGACTCTAGGGCACCAGACTCCTTGGCTCATTTTCAAACAAATTAGATCTTAAGTTTAATAGAAGTCGTTATTTAATGTATACATATGTATATTTTTTCTAAAATAGCACCTGTGGTTATGAATTTTAAACATGTTGACCAGTTTTGGTCCTAAATATTAGGGTAACCTGGATCAAATTATGCTGAGTTAATAGCATCCAACTAATGAAAGCTTCTTTGATTTTTCTTTCGTAAAGTGGTTTGGAATATCCATGAATCTTGGGCAATAATTAAGAAGTAACACATTGAGTTTGTTTTAAGTTTGACAATTCACTGAAACAGAAATCTAAGAATCAGATAAGATCTATGGCCTGATATCGTTGGGTTTTTAAATCTAGATGACTCTGATTTAGAAGTCAGCTCTGGGTTTTATTTTAGTAAGGAAGACTGGAATTAAAGAGTGGTCACTAGATTAAAGGTGAGATTTGGGGTAAGCAGCATCTTAAGTGATGCTCTGGTAAGCCAGAAGTTGTAGAAGGGCACAGCAGGTGGCCTGCCCCTTGCTCTCTAAGGGGCACTTTTAGTGTCACTTCATTACAGCTTTCAACTCTGGCAGGTGACAGAATGTAAGGTACAGGAAGGTAGCTTGGGATAGAGTAACCAGAACTTCTATGAAAACAAAACTTGAAAGACTTGAAACTTAGTGGTTTTCTTTTCTTTTTTAAATCCAGACATGCCCAGGTTTTAAAGGTCCTGGGATTTGAAAAGCCGAACCTCAAATTGCCATGGTTATAGTTAACTTTATACATTTGTGTCAGTGGACCAATATTCCAACTGCTCAGAATCTTGCCTCTTCTTTCTTCCATTTATTTTGTGGCTGTATGTTCAATGTTCCATCTTACCAATTTTTTTTAAACCAGCTTTTTCCTTTTTACAGTATTTCCTTACCGATTGCAGTAATGGACTAGGGTTCTGCTAGTGACCAGTTTTCAGTTTTGTAGGGAGATGTGACTCATTAAAAAAAACCCCAAGCTCAAGCAAAGTCAGCAGGACCAGGGGTGCTTAGGAGGTGTGGCCAATTGATAATGAGCTGGCTGCTGATTACTGTGCTCTAGGAGCTAGAAATTTCATTTACAGAAAAGTGGTTGGGGGGACTGTGGTGCTTTCTGCACTTAAACCCAGCACATGTGTTTGTCTGTTGAGTTCTTGGCTAGCCTGGGCTACATGAGTTCAGGAAAGCCAAAGATACACAGTGAGACCTTATCTGAAAGAAAAAGAAAGAAAAAGAGAAAAGGTGGCTGAAAAACTTGTTCTGTCAATAACTACAATTATTATGAGATTTGAAATTTGCTTCAGGTGTTCAAGTGGACTGTTTCCCCCTTGAAGGTCTCATCTCTTTACTTAATGATAGTATTTTTTTTTCATTTAAGACAGGTAATGGGTACATGGCAGAGGTGGCTGGACTCCAGGCCAGCCTGGGCTGCATAGAGATCCTGTATCCAAAAAAAGTTTCAGCTTTAGCACTTCTTTTTATAGTACACTTTTTTTTTTTAATACAAGTATTCAATCTTTTTTGGGGCCTTGAAATTATAGGCTAGGTTTTTTGTTGTGAAGCATAACTATCCAAAAATAAGTGGGATAAATTGTTCATTACAATGATTAAGACTTGACTTTAAAGAGGAAGTTGAGCTGAGGCCACATGGCTATCCTTTTACTCCCTGTCACTGGTAATTTTATACAAAGTGGCTAATGAGGTGTTAGAAGTAATACTTACTCTGAAAATGTGTCTCTTGTAG
Seq C2 exon
CGGAACGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGCAAAAGTGGAGTAGGCAACATATTCATTAAAAATTTGGACAAATCCATCGACAATAAAGCACTATATGATACGTTTTCTGCGTTTGGTAACATCCTTTCATGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283-Pabpc1:NM_008774:1
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=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: