HsaINT0073939 @ hg19
Intron Retention
Gene
ENSG00000197540 | GZMM
Description
granzyme M (lymphocyte met-ase 1) [Source:HGNC Symbol;Acc:4712]
Coordinates
chr19:547280-548677:+
Coord C1 exon
chr19:547280-547436
Coord A exon
chr19:547437-548541
Coord C2 exon
chr19:548542-548677
Length
1105 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CTGATTCCCTCTGTCCCCAGGAT
3' ss Score
12.14
Exon sequences
Seq C1 exon
GCAGCTCCTTTGGGACCCAGATCATCGGGGGCCGGGAGGTGATCCCCCACTCGCGCCCGTACATGGCCTCACTGCAGAGAAATGGCTCCCACCTGTGCGGGGGTGTCCTGGTGCACCCAAAGTGGGTGCTGACGGCTGCCCACTGCCTGGCCCAGCG
Seq A exon
GTGAGTACCCTGCCCTGCCCACCCCAGGGGTCCGGGGAATCCATCCGACGGCGCCCATTCTCTGCAGGGGGTGGGCTCTGGGAGATTTAGGCCCATTGTGGGACCCCCGTCCCCTCCCGGTGACGACTTAGGCAGGTTTAAGTGACCTGCGGCTGTGGGACTCCTGGAGAAGGTTTACTCCTTGCAAGAGGCACTGGCAGGGCCAGCTCCTTCCACACCGCAGCCTGGGTCAGAGCCTGGCTCCTTTCACGGCTGAGCCACAGTCCTGGTGTGGACAGAGTGCATTGTGTCTGTCCATTCACCTGCTGATGGACCCAACTTAGGCGGGGGCTTCTGCTATAAGGAAGGAGGGTCAGGTGGGGGTGTTTGCCACCTGTGGCCAGGAGGTCGAAGCCGGCCTTCGAGAGTGGCTCGGGAATCGACCTGGTTCCCGGGGATCAGGAAGCCGCTAAATGACCCATCATGGAGTTGCCCTACCTCAGGACTGGTCCGTCATACAGAGCCCAGATCAAGATGGTCAAAGTAACAAAAAGGGATCTGCCGGCTTGTGTAACTGCAAAGTCTAGGAGGAGGCCTGGCTTCAGGTGCGGCTTGATCCAGGTGCTCACAGGAGGCGCTGTGGAGCCCATCTGTCTCCCAGCTCTGCTGCACTACCAGGAAGCCTGTCTCACAAGGTGGAAAGATTGACCCTCCTCAGTCCCATGGAAAGAGGGCTTGGCTCTCTAAAGTTGGGGCACACTTAGGAGGATTGGCATGTGTCAACCCCTGTACAAATCACTGTGGTTGAGCCTGGGGCCCCAAGTGAAGGGAATTCCCAGGGCTGGTTTTCGTGAAGCTGTAGGCTTGGGGTTGGATTTTTGGACACACAGCCCTTGCCTGGGGCCAGGGCCGGGCAGAAGTCTGGGGCAGGGGTGAGAGCAGGGAGGGCTTCCTGGAGGAGGTGGGTTGCAAAGACACAGGGAAGGACTGGCCAAGCCAAGGCCTGTGAGGGGCAGCGGCTGTGAGTGATGGCCATGGACAACGGGCACAGTGGGGGCCGGGACTGCATGTGGCGGGTCGTCCACGCCGGGCCAGGCCGCAGCACCCTGATTCCCTCTGTCCCCAG
Seq C2 exon
GATGGCCCAGCTGAGGCTGGTGCTGGGGCTCCACACCCTGGACAGCCCCGGTCTCACCTTCCACATCAAGGCAGCCATCCAGCACCCTCGCTACAAGCCCGTCCCTGCCCTGGAGAACGACCTCGCGCTGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197540-GZMM:NM_005317:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(20.1=84.9)
A:
NA
C2:
PF0008921=Trypsin=FE(20.1=100)
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:
CTTTGGGACCCAGATCATCGG
R:
CTGAAGCAGCGCGAGGTC
Band lengths:
286-1391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)