MmuINT0125815 @ mm10
Intron Retention
Gene
ENSMUSG00000040478 | Prdm13
Description
PR domain containing 13 [Source:MGI Symbol;Acc:MGI:2448528]
Coordinates
chr4:21677481-21683538:-
Coord C1 exon
chr4:21683418-21683538
Coord A exon
chr4:21679948-21683417
Coord C2 exon
chr4:21677481-21679947
Length
3470 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
CTCTCGCCTTTCTTGCCCAGGGG
3' ss Score
8.49
Exon sequences
Seq C1 exon
ATCTTCTATCGGGCATTGCGAGACGTCCAGCCTGGGGAAGAGCTGACTGTGTGGTATTCTAACTCCTTGGCTCAGTGGTTTGACATCCCTACAACTGCGACTCCAACGCATGATGAGAAAG
Seq A exon
GTACTGCTCTGAGGTCTCCCCAACAGCGAGGGTGAGCAAGAGTAGAGTCCAGTTCTCCTGGATTGTGGAAGGTGAACACAGGCCTGAAGAATCTTTCTGTTTAGCTTTGTGGAAACTGAATTCATGCTCTTGACAAGGGAGAGAGGGAACTGCTAGCCTAGAGCTCATAAGCGAATGGTAATAAAAGTAGTAATCTGGTCCCCATGGCAGAGGAATACTCCTTACAAACTTCATGGGTCCTTCCTGTCCTATTTCATTCCGAATGACAAGTATTTACTCACTTAAGACACAATAAAGAAGATTTGATATGCTACAACAACTACATCCTGAATTCTAGACACCAAAGTTACAAGGATTACATCTTGAATTCTAGAGACCAAAGCTTAAACGTAGAATGCTTTTTAAAAGGCACAAGGGTACTCTTTCTCTGTAAGTTTTTCAGGAGAGCAGTGTATTCGATGGCATTTAGAAGCATTATAGAGCTTACAGCTGGTCCCTTGGCAGGTACTAACATCCTTCCTTGAAATGGAATTTATTCATTTCTGTTTAAGTCTACTTAAACAGAATCTGGGATGTCTCCCAGTTTCTTCTCAGATTTATTTGATTCCTTTCAAGCCAAGAGCCAATCCATGCAAATTAAGGCGCAGCAACGAAAAGGAAAATCATTTCAACCCCTCCACACAGCACTGAAGGTCATTTCCTGTGGAAAGAAGGCTGGGAAGAGCTGAAAGACTTAAGGTCTTGAAAGTCCACTCCCACCCTTCACAAGGCATCGCCTGTCCTGATCCCCAACCCCTTGAGAGTTGTTTGAGCATGTTCATTATTTCTCCAAAGAGGCTATTTATTTATAGACAACAAAAAACGTTCCAAAGTATTTTAATAAATCTCCTCCGGAACTGCTGTGCCACGGCCTCCATTTAGAAGCAGGTATATACTGATAAAAGTGTGGTAATTAGCAAACACTACATGCGCGGGACACATTATTCACAGCAATGAGTCATTTCACTTCACAGTGTCACTGTCCTCTGCAAATCAATTCTATTTGTTTAAAAATAGATTGGTATGTCCAATATTTATAAGAATTATACTGATATTGTTTGTTCCCTGAACCACATTCAGATTCTTCTGTCAATAATAAGTACTGCTGTCCTAGGGGGAACTCTCAGACTTGAAACTCCACAACAAATTGTTCCAGCACAGAACACTTTCACATAGGAATGACTAAACAGAAAAGCAACGTGTTTAATCATGTATTCTATTTCAGCCAACTGGTTTTATAAATGCCATAAGCCAAATGATAATAACAAATTTATAATTTTTCCTGTTAGGGAAGGTACATTGTACCTTGAACCTGATATTTTCTAGACTGGGCATGCCTAAAATCTTTAAAATTACATGAAGAGGGAGGAACAAAGTCATTTATGAAGCGTGTTTGGCTCACTTGGCAAGAGTTGAACCTTAGGGTCTGCAAAACCTGTTGATGAAGTTAAGTTGGAAAAGTAATATGTGGAATAACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAGCACATATGGACACACTTTTGTTACATTTTGAGAAGAGGAAGAAATAAGTAGGAATATCACCTGTTTTAACAATGCTGGCTAACTTAAGTTAGTTTCATTTCATAGAAAGATTTTTACTGCTCCTTCATTTTTAAGAACACAGCTTACTTGGCTTTGCATTGGCAGAGTCACTCCGGAACAAACAGAAAACTCTTGAAGAACTGCTACAAAAGACCTTATGAATTTCAGACACCCCCCCCCCCCCAAAAAAAAAAAAACTAAGGGGTCACTTCTCTTTCCAAGAGTTGTTTTAGTAAAACATCTTTTCTACATAAAATCCTGCTTTTCATAGGCAGCAGGAATATTGAGATGGTTTTGCCTAAGTCTTCAACCAACAACTGAGATAGACTGTTATAGATAAATCCTTATCTCCGCATTTCTCCCAGGTCTCCTTTGACCTCTTGTGGAATAAACTCCGCCCACCCCTCCTTGAGCTTGTTACGTAGCCCCGGCTGGTCTGGAACTCACTATATAGCTCAAGCTGGCCTCGAATAGCTCAAGTTGGCCTCGAATTCCGAACTCACAAAGATCCGCCCGCCTTTGCTTCCCAAGTGCTAGAATTAAAGGCATGTTTCATCATGACGGGTTCTGTAGCAAGGTTTTAGAAGTATGAGCAGAGGACCTAAAGAGGGAGCATGTAATGTTTCTAGTAAATCTCACAGACCTACAATGTACTTTGGAATTTCCTCATGGTCCAATCAACTTTTCTCACAGACATCTTAAGTATTATCAGTTAATCACTTTAAAAATAAACTGCATTGTATGCACACTAGCACGTAGAAATTAGTTTCTAGCACTCAATTAGTAGCTATCTCATGTACCTGTCTCTGGATTGTGTTTACAGACCCTAGCAAGTCAAAAACAGTTATGTGAGAGACACACAGAATTGACGCTGCACGTGCACACATGCACAGCACTTGTGGTAGAGAAATCTGCACTTTAAAAGGGGGAGGACCTTTCTCATTTTTATATATTTATTAAATGAATTATCTTGCTTAAGTGTTTTCTAAGCTTATATCTGTGCACCTATCTAGGAGTTAATTAGCCACCAGGTAAAACAACAGAAAAGCCAATGCTATGCCATCCTCAGAATATCAGCATCCATTCCAGAATATCAGAAAGTAGTAGTCCCCCCCCCCCAATCCAATTAGATAAAGTTAAAATAGGAAATAAGGGTGCAAACCATCATCCTTATGTGGGGATTCATTTGGTCACGCTCCAGGAAAACCTCAAGCAAATATTTTAAGTCTGGGAGGGGGTGAAAGGGCGGAGAGAGGACACAAAAGACATTGTTATATGAAAAGGAATGATTACATATGGCCCATACATACAGGATATTGTCTCGCCTGGTAATGAGGCGCTCACGACTATTAGATTGGCCTTTGTTCAGTTTATCCAAACTCCTTGACATACGCCACCTATTCTGTAAACGCCAACAGATGGGCACAGGCACAGCACAGCCTCAACACTTGATTTAAGGCAACAGCTGCTCTCTGTTCTTCCAGGCTAGCCTTCCTGAGCAGGGCTCTTCCAAAGGAGATTTACTGTGAGGGCTTGGTGGAAATCTTCACTGGAAAGGTCCAGGTCACCTATTTTGCTCTTTAAGTAGGCCTTTGAGGATGGAAGTGACAAGGGTTGGCCATTTACACGCCTTGGGAGGTTCTTGATAGGGTTGCTAAACTTTATCTCTTGGCCCTAAGACCTTCATCCTTTACCCTCGCTTCTGCCACCTCGCAGGTCAAACCCGGGCTATGCCTGCTGTGCCTGCTGGGCTGGAGCTTTCCTTCTGGCTCCCTAGCTTCTCACTTGTTACTCTCGCCTTTCTTGCCCAG
Seq C2 exon
GGGAGGAGCGCTACATCTGCTGGTACTGCTGGAGGACCTTTCGCTACCCTAACAGCCTCAAGGCACACCTGCGGTTCCACTGCGTCCTCAGTGGCGGCGGGGGCCGTGCTTTCCTGCCCCAGGAGCACGCGGCCCGGCCCGGCGCTTCCCCGGTGGCAGAAGGCCTCGGCCTCCCTCCGAAACCCACCGTCCCGGACTTGACGGCGCCCGTCCAGGCAATCGCTTTGCGACCCCAAGCTCCGGCCGCTCAGCTCGCCCAGGCGTGCGGGGCGCGGGAGAGCATCAAGCGGGAGGCTTCCCTGGCGCCCCTGGCCACCTCCCCGCCGCCGGGCAAGTGGGGAACGCCCAAGAAGGGCAAGGAGCAGCCGGACCGCGCGCACAGTCAATTCCTGGGGATAGTGGGCGGCTCCTCGGGCGGCGGCGGAGGCCTGCCATTCTACCCAGGCGTGCGCTCGGCTTTCAAGCCGGCCGGCCTGGCCCGGGCGGCTGCGCAGAGCGACCCCTACCGGGAAGAGGGCGGCGGCAAGGGACCGGGGCTGGCGCTAGGGCGGCTGCTGGGCGGGGGCCGGGCCGGCGGGCGTCCGGGCAGTGGGGAGAGCCCGGCGGGCCACCACCACCATCACCACCACGCTCACCACCACCACCACCACCATCCCAAGTGCCTGCTGGCCGGGGAGCCGCCGCCGGCGGGCCTGCCGTGTCCCGGGGCCCTGAGAGCCTTCCCCCTGCTCGCCGGCCACCCGGAAGAGGCGTCGGCCTTCAAGCACGTGGAGCGGGCTCCGCCCGCCGCCGCCACCACCTCCCTGCCCTCCGCGCGCTACGCCGCTCTCCCGGCGCCCGGGCTCCCTGTGGAGCGCTGCGCGCTGCAGCCCCTCGACGGCGGCAGCCTCAAGGCTTACCCCGGCGGCGGTGGCGGCGGCGAGTGCAGCCCCCTGCCCGCCGTCATGCCGGCCTTCACGGTGTACAGCGGAGACCTGCTCTACGGCCCTCCGGCCGCCTATTACCCTCTCAAGCTGCACTTGGGCGGGCTGCTCAAATACCCCGAGTCCATCTCCTATCTGAGTGGCCCCGCGGCGGCAGCGGCGGCGGCGGCAGCGGCAGCGGCGGCGGCGGCGGCGATCGGGCCGGCCGAACTGGGCTCCCTGGCCAGCATCGACCGCGAGATCGCCATGCACACACAGCAGCTGTCCGAGATGGCAGCCGGGAAGAGTCGCGCCCGCCTGGACTCGGGGACGCTGCCTCCAGCCGTAGTGGCGGCGACGGGCCCCGGGGGTGGCGGCGGTGGCGGGAGCGCGGCAGGCAAGCCCAAGACAGGCCACTTGTGCCTCTACTGTGGCAAGCTGTACTCGCGCAAGTACGGGCTCAAGATCCACATGCGGACGCACACGGGCTACAAGCCGCTCAAGTGCAAAGTGTGCCTGCGGCCCTTCGGCGACCCCAGCAATCTCAACAAGCACATCCGACTCCACGCCGAGGGCAATACGCCCTACCGCTGCGAGTTCTGCGGCAAGGTGCTGGTGCGCCGCCGAGACCTGGAGCGTCACGTCAAGTCCCGCCACCCAGGCCAGAGCCTGATGGCCAAGGCGGGCGACGGCCCGGGCCCGGAGCCCAGCTATGCTCTGGAGCCTGGGGATCCCAAGAGCGAGGACAGTGATGTGGATGTCTGCTTCACTGACGATCAGAGCGACCCCGAGGCTGGGGGTCGTGGCGAGCACGACTCCTAACGCGCCTTCCAGGGACTGAGCAGGGACGAGGACACAGTAGAGAGTGAAGTGGGGACAAGAAGGGCTTCATTGATATTGTCGCAATTCTGGGGATGGTGTCGGATTAGGAACAGTGAGCCGCTCCAGTTCTCGAGTGGAGCAAAGTTTAACGAAGGGTTGAAGAAACACAGCCAACTAACAGCACATAGGTTGTGGTTCTCTATCATTAAGACCCCTAGACTCTGGCATAGCCTCTCATTCTGAAAGCATTCTGGCCTTGAGGTTCAGGATCACGTCAATATAAGCATCTCAGTGCGCTCAAAGGTGATGATTTTTACTGCCACACATTTTTAAAACGCTCTTGTCTGTGGAGGAAATCGTGCCTTTTGAAAAGATGTTCCGTGTGAATTTTATGTTAAGCATTTCACTGCATAGCAAGCAAAACAGTAGATGTGACACCCACACACCTGTTTCCGTTTCCTATCTGTTCTCCTGTCAAAGAACACTCCTTGCCACATTGAGTATATCGTGGTAGTGGATGTATAAATTGGTCAAGTTGCAATTATTTATGAGAGAATAATGATAAATGTAAAATGACGCATGAATATAAGAGCACGCAATATATAAATTTAAAAAATCCTATTTGGTAGAGTCCAAATGTTTATGTTGTTTTATAATGAACGATGTACAGTGGATACAGTACTTTGCCCTTGCTTCCATTTTGTGCAATCTGTAAGAATAATAAAGATACAAAGGAGAGTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040478:ENSMUST00000076206:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.146 A=NA C2=0.444
Domain overlap (PFAM):
C1:
PF0085623=SET=PD(50.0=46.3)
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=4.2),PF134651=zf-H2C2_2=WD(100=4.3),PF134651=zf-H2C2_2=WD(100=4.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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
- 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