MmuINT0132394 @ mm9
Intron Retention
Gene
ENSMUSG00000061898 | Rbak
Description
RB-associated KRAB repressor [Source:MGI Symbol;Acc:MGI:1927369]
Coordinates
chr5:143933868-143937810:-
Coord C1 exon
chr5:143937715-143937810
Coord A exon
chr5:143936738-143937714
Coord C2 exon
chr5:143933868-143936737
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
AAATCAGTAAAGTTTATGACCCCAGAGAAGGAATTGAGGAAATTGGCGAGAAACATCTGCAGTGCGATGATGATCCCTACTGCTGGAGAGCTGAGAAGGGGGCTGCTTTTGATGAAGCCTACACCCTCGAAACAGCCCTCATTTCCCCCAGCTCAGGTGCTCACAGCTGTGTCTCCTGTGGGGAGACCCTGGAGTCTGTTTCAGAACTGATTAGCAGTGACGGAAGCTATGCACTGGAGAAGCCCAGCATGTGTTTTGAGTGTGGGAAAGCATACGGAGAAAGCCTTGAAGACTTCAACCAAGATGAGGGTAACTCCTCTCAACACGATGAAAATATTTTGCAGAAAGTCACCATTTTGGAGAAACCCTTTGCTTATGAGTGCATGGAAGCCTTAGACAGTGAAAGTGTTTTCATGGCTCGTGAGAGAGCTTACATGGGGGAGAAGCCCTATGACTGGGGAGACTCTGGACCAGACTTCATCCAGATGTCGGACTTCAGTACATATCCGAGATCACAAATGGAACTGAAGCCCTTCGAATGTACACAGTGTGGGAAGTCCTTCTGTAAGAAGTCCAAATTCATCATCCACCAGAGAGCTCACACAGGAGAGAAGCCGTACGCTTGTAGTGTGTGTGGAAAGTCCTTCAGTCAAAAGGGAACCCTCACTGTACATCGGAGATCGCACTTAGAGGAGAAGCCCTATAAGTGTAATGAGTGTGGGAAGACCTTTTGTCAGAAGTTACACCTCACACAGCACCAGAGGACTCACTCAGGAGAGAAGCCCTATGAATGTAGCGAGTGCGGGAAGTCCTTCTGCCAGAAGACACACCTCACTCTCCACCAGAGGAATCACTCAGGCGAGAGGCCCTACCCGTGTAATGAATGTGGGAAATCCTTCTCCCGGAAGTCTGCCCTCAATGACCATCAGAGGACACACACAGGAGAGAAGCTCTATAAGTGTAATGAGTGTGGGAAATCCTACTACCGGAAGTCCACCCTCATTACACACCAGAGGACACACACAGGGGAGAAGCCCTATCAGTGTAGTGAGTGTGGGAAATTCTTCTCTCGGGTGTCGTACCTCACCATACACTATCGGAGCCATTTAGAAGAGAAACCTTACGAGTGTACAGAATGTGGGAAAACCTTCAATCTAAACTCTGCTTTCATTAGGCACTGGAAGGTCCATGCAGAAGAGAGAGTCCAGGAGTGTGGCGAGTGTGGGAAGCCATCCCCGCTGCAGTGTGCCCCTGATCACACAGGCGACCTAGGAGAGAAGCGCTATGAGTGTAATGAGTGTGGAAAGACCTTCCTTGACAGCTCGGCCTTCCATAGGCACCAGTCCGTCCCTGAAGGGGAGAAAACTTACGAGTGTAATATATGCGGAAAGTCCTTCTCGGATTCGTCATGCTACACTGTGCACTACAGAGGTCATTCCGAAGAGAAGCCCTTCGGGTGCAGTGAATGTGGGAAGACCTTCTCTCATAACTCATCCCTCTTCAGACATCAAAGGGTCCACACCGGCGAGAAGCCGTACGAGTGTTACGAATGTGGGAAGTTCTTCTCTCAGAAGTCGTATCTCACTATCCATCACCGGATCCATTCGGGAGAGAAGCCCTACGAGTGCAGCAAGTGTGGGAAAGTGTTCTCGCGGATGTCGAACCTCACCGTACACTACCGAAGCCATTCAGGAGAGAAGCCGTATGAGTGCAACGAGTGTGGGAAAGTCTTTTCTCAGAAGTCGTACCTCACCGTGCATTACCGGACTCATTCAGGAGAGAAACCTTATGAATGTAACGAATGTGGGAAAAAATTCCACCACAGATCAGCCTTCAATAGCCATCAGAGAATTCATAAAAGAGGCACTGTAAATGTACTCACTGTAGAAAAGCTCTGACATGCCAAGGTTTTTAAATTTTTTTTTGGTTTTGGTTTTGGTTTTTTTGAAACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCATTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGTGCACCACCACTGCCCAGTGACATCTCAGTTCTTAAGAAAAGCATTTGGTTATAGTGAACATTGGAAGTCCAACAGGTAGTCAAGGGTGGACCCCCCTCAACCCCCCCCCCCAATTTTCAATATATGTGGTGCTGGGATTCTGGGCCTTTTGCATGCTATAGACATTCTGCAAGATTCACGAGCTGAGCATCCACGCTCTTGAGTGTGGAGTCCTAAAACAAAGTCCATTTTAACTTGAGCTTTCAGAGAGGAATCTGTGAAGCAACCCATGACCGTATGACTTATGGGACACTAGGTCATCTTTACAGGAGTGAACCTTTGAAAGTATTTAATATTTATTTTTATTTAAATCGTATTTACATATCAGGGAGTTCTGCTGTGAGCTGTCAGCTCCTGAGTATAACTCGCCTTGGAAACGCACACTAAAAGCCATATTTCTGACCGACGTTACCACGGGTGTTCATGGAAAAGATGCAAGAAGCTATGAGTTCCGAATAAACTTATAAAATGAAGTCATGAAGCCAGCAGTTGAGCATGAGGGTGACTGAAACACGGCACTTCTGCTGTTCTAGACACGCAATTGAACAGTCTCTATGCAATGTTTCGCAATCTCGGCTTTGAATCATTTGTGAGAACATGTCAGCAAGGATTAAAATGACTGTTACAGTGGGTACATGGGTGGGATGTGCTAGCTGATAGGGAAGTACATAGCTTTCTATGTCGGTGCTTACCCGTAGAGTGGTTTTTGTAAAAATATTTTCAACTGGAATTGAGCAAAAAAATTTTTTAAATACTATTTTGATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061898-Rbak:NM_001045482:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.265 A=NA C2=0.039
Domain overlap (PFAM):
C1:
PF0135222=KRAB=PD(0.1=0.0)
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=4.1),PF134651=zf-H2C2_2=WD(100=3.9),PF134651=zf-H2C2_2=WD(100=3.9),PF0009621=zf-C2H2=WD(100=3.8),PF134651=zf-H2C2_2=WD(100=4.1),PF134651=zf-H2C2_2=WD(100=4.1),PF0009621=zf-C2H2=WD(100=3.6),PF0128613=XPA_N=WD(100=3.6),PF0009621=zf-C2H2=WD(100=3.8),PF134651=zf-H2C2_2=WD(100=4.3),PF134651=zf-H2C2_2=WD(100=4.3),PF134651=zf-H2C2_2=WD(100=4.3),PF134651=zf-H2C2_2=WD(100=4.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: