HsaINT0073941 @ hg19
Intron Retention
Gene
ENSG00000197540 | GZMM
Description
granzyme M (lymphocyte met-ase 1) [Source:HGNC Symbol;Acc:4712]
Coordinates
chr19:548922-549919:+
Coord C1 exon
chr19:548922-549185
Coord A exon
chr19:549186-549629
Coord C2 exon
chr19:549630-549919
Length
444 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCGGTGTGTCGTCCCTGCAGGGT
3' ss Score
11.05
Exon sequences
Seq C1 exon
CTGGACGGGAAAGTGAAGCCCAGCCGGACCATCCGGCCGTTGGCCCTGCCCAGTAAGCGCCAGGTGGTGGCAGCAGGGACTCGGTGCAGCATGGCCGGCTGGGGGCTGACCCACCAGGGCGGGCGCCTGTCCCGGGTGCTGCGGGAGCTGGACCTCCAAGTGCTGGACACCCGCATGTGTAACAACAGCCGCTTCTGGAACGGCAGCCTCTCCCCCAGCATGGTCTGCCTGGCGGCCGACTCCAAGGACCAGGCTCCCTGCAAG
Seq A exon
GTGAGGGGCGCCCGGGTGGGGCTGGGGGAATGAGGCTGGCGGGAGGGCCGGGGCCAGGGCAGCCGCCGGGCAGGTTCCTGGCTCTCCCGTTCTCTGGGGAGTCCTGTCAGGGGCTGGGGGGCGGGGAAGCACTGGCAGGGGTCCCGTTTCTCAGGTGCAGAAACTGAGGCTCAGACAGGTTTAGCAACCTGCGCAAGACCACACAGCCGGGAAGCGGCAGAGCTGTGACTTCTGCTCCAGCCAAGACGGTCCGGCGGGGGAAGAAGGAGCAGGGTTCACAGGGCCAGCGGGAGATGGGGAGGGGACACGCGTGGGCCGGGAGCAGCCCCTGTGTCTCCTTGAGCCTGGGGATAACAGGCCTGGCCCTGCTCCCCTCGGCGGGCCCTGCTCCCCTCGTCCCCTCAGCAGGTGCAGAGGCTGAGCTGCGGTGTGTCGTCCCTGCAG
Seq C2 exon
GGTGACTCGGGCGGGCCCCTGGTGTGTGGCAAAGGCCGGGTGTTGGCCAGAGTCCTGTCCTTCAGCTCCAGGGTCTGCACTGACATCTTCAAGCCTCCCGTGGCCACCGCTGTGGCGCCTTACGTGTCCTGGATCAGGAAGGTCACCGGCCGATCGGCCTGATGCCCTGGGGTGATGGGGACCCCCTCGCTGTCTCCACAGGACCCTTCCCCTCCAGGGGTGCAGTGGGGTGGGTGAGGACGGGTGGGAGGGACAGGGAGGGACCAATAAATCATAATGAAGAAACGCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197540-GZMM:NM_005317:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(38.8=100)
A:
NA
C2:
PF0008921=Trypsin=PD(19.6=81.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTAACAACAGCCGCTTCTGGA
R:
TTATTGGTCCCTCCCTGTCCC
Band lengths:
356-800
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)