HsaINT0073928 @ hg19
Intron Retention
Gene
ENSG00000100453 | GZMB
Description
granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) [Source:HGNC Symbol;Acc:4709]
Coordinates
chr14:25101064-25101665:-
Coord C1 exon
chr14:25101530-25101665
Coord A exon
chr14:25101325-25101529
Coord C2 exon
chr14:25101064-25101324
Length
205 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TCTTGCCTCTTCCCCACCAGCTG
3' ss Score
8.78
Exon sequences
Seq C1 exon
CTCCATAAATGTCACCTTGGGGGCCCACAATATCAAAGAACAGGAGCCGACCCAGCAGTTTATCCCTGTGAAAAGACCCATCCCCCATCCAGCCTATAATCCTAAGAACTTCTCCAACGACATCATGCTACTGCAG
Seq A exon
GTGAGGCACACTCCTGCCACTCTTGCTCTTCTTGGTCCAGTTGGTTCCACTCCCCCTGGAATGCCGGCCCTTCCCTCCTTTCCATCCTGGCCTCTTGGTTAGTTCCTATGCCTCAGAGGAGAGGGAAGATTGTGCAGCCCCATCACTGTGTCGGGGCCCAGAAGTTCGTTGGCTGACCTGGACTTTCTTGCCTCTTCCCCACCAG
Seq C2 exon
CTGGAGAGAAAGGCCAAGCGGACCAGAGCTGTGCAGCCCCTCAGGCTACCTAGCAACAAGGCCCAGGTGAAGCCAGGGCAGACATGCAGTGTGGCCGGCTGGGGGCAGACGGCCCCCCTGGGAAAACACTCACACACACTACAAGAGGTGAAGATGACAGTGCAGGAAGATCGAAAGTGCGAATCTGACTTACGCCATTATTACGACAGTACCATTGAGTTGTGCGTGGGGGACCCAGAGATTAAAAAGACTTCCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100453-GZMB:NM_004131:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.268 A=NA C2=0.241
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.5=100)
A:
NA
C2:
PF0008921=Trypsin=PD(17.2=41.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAGACCCATCCCCCATCCA
R:
CCCACGCACAACTCAATGGTA
Band lengths:
296-501
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)