MmuINT0132394 @ mm10
Intron Retention
Gene
ENSMUSG00000061898 | Rbak
Description
RB-associated KRAB zinc finger [Source:MGI Symbol;Acc:MGI:1927369]
Coordinates
chr5:143172186-143176131:-
Coord C1 exon
chr5:143176036-143176131
Coord A exon
chr5:143175059-143176035
Coord C2 exon
chr5:143172186-143175058
Length
977 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TCCATCTCACTCCTTTTCAGAAA
3' ss Score
9.53
Exon sequences
Seq C1 exon
GGTATGACGTTACCAAGCCAAACATGATTATTAAGTTGGAGCAGGGAGAAGAGCCCTGGACAGTGGAAGGTGACCGCCATGCTCAGAGGCATTTGG
Seq A exon
GTAAGTGAATAGAGTGAAATTTTAGAAAGTGTTCCTTTTTAAATTAATTTTGTAGGGGAAGCTTCTGAAACCTAGTGCTTTACAGCAAAGGAAATCCAGAAACGTGCAGGTTTATTTGTATTTGGAATTAAGAGACAATTAAGGAAAAAACTATGAGGGAAGAAGACAGTAGGTTAGGGAATGTGAGTCTCCCCAGCAGAAAGAGTGGACAGAAAGGAGATTCAAGACTGACCGGAGTGAGCGTTCGCTTTATATCACAAATGTCTGAGCCACGGTGGAGGGGCATGAAACTTTCATAATGTTTTTACTAATGTGTGGGGTCAAAAGGCAAAGATTTCACTGAATGTGGTGGCTCAGGTCTGTAGTTCCAAAACTCCAGGTAAGGCAGGCAGATTGCTGACAGTTTAAGGCCAACCTGGGCTAAATAGAAACACACTGTTTCAAACAAAAGCAAAGATTTCAGAAGTGACTAAGGTGTAATCTCCCATGAGACGTAGACCCATGGACGTAAATGCAGAAGTGTCTAAGGTATAATCTCCCAAGTGATGGGTTACTATTTGATAGAAATAGCAATCTGGGTCTCCCAAACACAGGCCATATTAAAACATTTCTTTTTCATATGTCCAATAATTATTTCCCCTGCTTCCCTTTGCTGCGAGTCCTCCCACTGTGCGTCCTCTGTGTCTGTCTGTGTCTGGTGCCCTTTCAGTAACTGTGCTTCCTGCTCATCATTTCTTAGGTCAAAGTTGTAAAGGTAATATTTGTAACGTAAGGTGCTTGCTTCCATTGTAAATTGATTCTCTTCCCATTTCTTACCCACCCTGCATATACACACTCAGATTACAGATTATAAATGAAAGGAGAAGGAGACCTGTGCATTCATAATTGCTTTTACTCACAGATTGTCAGAAAATCCGACATTTAGGTAGCTTGTATACTCATGCTGACAGCATTTGTTCCATCTCACTCCTTTTCAG
Seq C2 exon
AAATCAGTAAAGTTTATGACCCCAGAGAAGGAATTGAGGAAATTGGCGAGAAACATCTGCAGTGCGATGATGATCCCTACTGCTGGAGAGCTGAGAAGGGGGCTGCTTTTGATGAAGCCTACACCCTCGAAACAGCCCTCATTTCCCCCAGCTCAGGTGCTCACAGCTGTGTCTCCTGTGGGGAGACCCTGGAGTCTGTTTCAGAACTGATTAGCAGTGACGGAAGCTATGCACTGGAGAAGCCCAGCATGTGTTTTGAGTGTGGGAAAGCATACGGAGAAAGCCTTGAAGACTTCAACCAAGATGAGGGTAACTCCTCTCAACACGATGAAAATATTTTGCAGAAAGTCACCATTTTGGAGAAACCCTTTGCTTATGAGTGCATGGAAGCCTTAGACAGTGAAAGTGTTTTCATGGCTCGTGAGAGAGCTTACATGGGGGAGAAGCCCTATGACTGGGGAGACTCTGGACCAGACTTCATCCAGATGTCGGACTTCAGTACATATCCGAGATCACAAATGGAACTGAAGCCCTTCGAATGTACACAGTGTGGGAAGTCCTTCTGTAAGAAGTCCAAATTCATCATCCACCAGAGAGCTCACACAGGAGAGAAGCCGTACGCTTGTAGTGTGTGTGGAAAGTCCTTCAGTCAAAAGGGAACCCTCACTGTACATCGGAGATCGCACTTAGAGGAGAAGCCCTATAAGTGTAATGAGTGTGGGAAGACCTTTTGTCAGAAGTTACACCTCACACAGCACCAGAGGACTCACTCAGGAGAGAAGCCCTATGAATGTAGCGAGTGCGGGAAGTCCTTCTGCCAGAAGACACACCTCACTCTCCACCAGAGGAATCACTCAGGCGAGAGGCCCTACCCGTGTAATGAATGTGGGAAATCCTTCTCCCGGAAGTCTGCCCTCAATGACCATCAGAGGACACACACAGGAGAGAAGCTCTATAAGTGTAATGAGTGTGGGAAATCCTACTACCGGAAGTCCACCCTCATTACACACCAGAGGACACACACAGGGGAGAAGCCCTATCAGTGTAGTGAGTGTGGGAAATTCTTCTCTCGGGTGTCGTACCTCACCATACACTATCGGAGCCATTTAGAAGAGAAACCTTACGAGTGTACAGAATGTGGGAAAACCTTCAATCTAAACTCTGCTTTCATTAGGCACTGGAAGGTCCATGCAGAAGAGAGAGTCCAGGAGTGTGGCGAGTGTGGGAAGCCATCCCCGCTGCAGTGTGCCCCTGATCACACAGGCGACCTAGGAGAGAAGCGCTATGAGTGTAATGAGTGTGGAAAGACCTTCCTTGACAGCTCGGCCTTCCATAGGCACCAGTCCGTCCCTGAAGGGGAGAAAACTTACGAGTGTAATATATGCGGAAAGTCCTTCTCGGATTCGTCATGCTACACTGTGCACTACAGAGGTCATTCCGAAGAGAAGCCCTTCGGGTGCAGTGAATGTGGGAAGACCTTCTCTCATAACTCATCCCTCTTCAGACATCAAAGGGTCCACACCGGCGAGAAGCCGTACGAGTGTTACGAATGTGGGAAGTTCTTCTCTCAGAAGTCGTATCTCACTATCCATCACCGGATCCATTCGGGAGAGAAGCCCTACGAGTGCAGCAAGTGTGGGAAAGTGTTCTCGCGGATGTCGAACCTCACCGTACACTACCGAAGCCATTCAGGAGAGAAGCCGTATGAGTGCAACGAGTGTGGGAAAGTCTTTTCTCAGAAGTCGTACCTCACCGTGCATTACCGGACTCATTCAGGAGAGAAACCTTATGAATGTAACGAATGTGGGAAAAAATTCCACCACAGATCAGCCTTCAATAGCCATCAGAGAATTCATAAAAGAGGCACTGTAAATGTACTCACTGTAGAAAAGCTCTGACATGCCAAGGTTTTTAAATTTTTTTTTGGTTTTGGTTTTGGTTTTTTTGAAACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCATTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGTGCACCACCACTGCCCAGTGACATCTCAGTTCTTAAGAAAAGCATTTGGTTATAGTGAACATTGGAAGTCCAACAGGTAGTCAAGGGTGGACCCCCCTCAACCCCCCCCCCCAATTTTCAATATATGTGGTGCTGGGATTCTGGGCCTTTTGCATGCTATAGACATTCTGCAAGATTCACGAGCTGAGCATCCACGCTCTTGAGTGTGGAGTCCTAAAACAAAGTCCATTTTAACTTGAGCTTTCAGAGAGGAATCTGTGAAGCAACCCATGACCGTATGACTTATGGGACACTAGGTCATCTTTACAGGAGTGAACCTTTGAAAGTATTTAATATTTATTTTTATTTAAATCGTATTTACATATCAGGGAGTTCTGCTGTGAGCTGTCAGCTCCTGAGTATAACTCGCCTTGGAAACGCACACTAAAAGCCATATTTCTGACCGACGTTACCACGGGTGTTCATGGAAAAGATGCAAGAAGCTATGAGTTCCGAATAAACTTATAAAATGAAGTCATGAAGCCAGCAGTTGAGCATGAGGGTGACTGAAACACGGCACTTCTGCTGTTCTAGACACGCAATTGAACAGTCTCTATGCAATGTTTCGCAATCTCGGCTTTGAATCATTTGTGAGAACATGTCAGCAAGGATTAAAATGACTGTTACAGTGGGTACATGGGTGGGATGTGCTAGCTGATAGGGAAGTACATAGCTTTCTATGTCGGTGCTTACCCGTAGAGTGGTTTTTGTAAAAATATTTTCAACTGGAATTGAGCAAAAAAATTTTTTAAATACTATTTTGATAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061898:ENSMUST00000165318:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.303 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0135222=KRAB=PD(0.1=0.0)
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=3.9),PF134651=zf-H2C2_2=WD(100=3.8),PF134651=zf-H2C2_2=WD(100=3.8),PF0009621=zf-C2H2=WD(100=3.6),PF134651=zf-H2C2_2=WD(100=3.9),PF134651=zf-H2C2_2=WD(100=3.9),PF0009621=zf-C2H2=WD(100=3.5),PF0009621=zf-C2H2=WD(100=3.6),PF134651=zf-H2C2_2=WD(100=4.1),PF134651=zf-H2C2_2=WD(100=4.1),PF134651=zf-H2C2_2=WD(100=4.1),PF134651=zf-H2C2_2=WD(100=4.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTGGAGCAGGGAGAAGAGC
R:
TCTCCGTATGCTTTCCCACAC
Band lengths:
343-1320
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