MmuINT0075439 @ mm10
Intron Retention
Gene
ENSMUSG00000015437 | Gzmb
Description
granzyme B [Source:MGI Symbol;Acc:MGI:109267]
Coordinates
chr14:56258856-56260442:-
Coord C1 exon
chr14:56260182-56260442
Coord A exon
chr14:56259563-56260181
Coord C2 exon
chr14:56258856-56259562
Length
619 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
TGTATCCACTCAATTCACAGGGG
3' ss Score
7.85
Exon sequences
Seq C1 exon
CTGAAGAGTAAGGCCAAGAGGACTAGAGCTGTGAGGCCCCTCAACCTGCCCAGGCGCAATGTCAATGTGAAGCCAGGAGATGTGTGCTATGTGGCTGGTTGGGGAAGGATGGCCCCAATGGGCAAATACTCAAACACGCTACAAGAGGTTGAGCTGACAGTACAGAAGGATCGGGAGTGTGAGTCCTACTTTAAAAATCGTTACAACAAAACCAATCAGATATGTGCGGGGGACCCAAAGACCAAACGTGCTTCCTTTCGG
Seq A exon
GTAAGTTGGGTTGCAGTCCCCTCTGGGCTAAGTGGGAGGGGAAAAGGAATCTGGGACCTAGAGACCCAAATATCAAGGGACTCCTTTACCCACTGGCTGTGATCTTTCTCCCTGGGAACAGCAGGTACTAGTAATGAACTGGGGCCCCCAGAGCTGACTAGGAGCCTCTGCTGAAGGTAGCTTGTACAAAAGGAGGTGTTGGCAACACAGTACCTGTCCCAGGCCCAGGCTGTAGAAAGCTGGGCTCCCTGGGTGTGTCATAACCACACCCATGTGTCTCCTCTGAGCAGACACACACTTTGTCAGTGGGCTTCCCCTCCATGCTCACACCTGGCCCACTCACTGTCCCCATGTCCTTAAACAACAGCCTAGAGACGAGGGTCCCACACACCTTCCTAGAGCGTGGATCACAGACCTGGGGAAAGGGCAGAGGCTGCCTCAGGAGGGAGGTGCAGCCCTAACCATGTCCACAGTCAGAGCTGGGAAGGCCGGGGGCCCCAGGACTGTCCTCTGACCTCCCATAAGCATAAATCATGCTTCTCTGGGAGGAGCCTTGACATGAGGAGGTTGGGACCAGGGTGAACAACAGCTCAGTGCCTTGTATCCACTCAATTCACAG
Seq C2 exon
GGGGATTCTGGAGGCCCGCTTGTGTGTAAAAAAGTGGCTGCAGGCATAGTTTCCTATGGATATAAGGATGGTTCACCTCCACGTGCTTTCACCAAAGTCTCGAGTTTCTTATCCTGGATAAAGAAAACAATGAAAAGCAGCTAACTACAGAAGCAACATGGATCCTGCTCTGATTACCCATCGTCCCTAGAGCTGAGTCCAGGATTGCTCTAGGACAGGTGGCAGGATCTGAATAAAGGACTGCAAAGACTGGCTTCATGTCCATTCACAAGGACCAGCTCTGTCCTTGGCAGGCCAATGGAACACCTCTTCTGCCACCATGCTGTGACAACCCAACTGACATCTTCCTATGGAAGTTTGCCCTCTCCACAAAAGAAGTAGAATGTTTGCATTGGAGCTGGGCATGCTCTGCTTCCCCTCAGTGCCCCGAGAATGTTATCTAATGCTAGTCATCATTAATAGCTCCCTACAGAACTTTCATACAGTTGCACCCAAGTTGCTGATGTGTTCTCTAGAATAGAGCAAGAAATAGTAAACAGAATTCCTTTTGCCTCTCTGTACTATTTTCCCCCAAATACCAAGATTTGTATGTTTTATAAAGCTAATTTCCTTATCAAATGACATCTTTTAATTTTTACATTAATGGCTTATTTTCAAGGTACAACCTGATTTTTTTATGGACAAAAATGATGTAAAATCAAATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015437:ENSMUST00000015581:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(39.1=100)
A:
NA
C2:
PF0008921=Trypsin=PD(17.7=81.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GGCCAAGAGGACTAGAGCTGT
R:
GTGAAAGCACGTGGAGGTGAA
Band lengths:
342-961
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