DreINT0041107 @ danRer10
Intron Retention
Gene
ENSDARG00000052702 | capn1a
Description
calpain 1, (mu/I) large subunit a [Source:ZFIN;Acc:ZDB-GENE-040426-1263]
Coordinates
chr13:42572682-42572917:-
Coord C1 exon
chr13:42572832-42572917
Coord A exon
chr13:42572757-42572831
Coord C2 exon
chr13:42572682-42572756
Length
75 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
GGTGTTTGTTCGCTCTCCAGCTC
3' ss Score
7.03
Exon sequences
Seq C1 exon
GTGGAGTACAGGGGGCGGATGGAGAGGCTTATCCGCATCCGTAATCCTTGGGGTCAGGTAGAATGGACCGGAGCCTGGAGTGATAA
Seq A exon
GTAAGTAATAACATAAAAAGAACTATTCATTTCAGCTCATGTCATTGAGTAAGAAGGTGTTTGTTCGCTCTCCAG
Seq C2 exon
CTCTCCTGAATGGGATGAGATTGATCCATCAGAGAAGGACGACTTGCACTTACAAATGGAGGATGGAGAGTTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052702:ENSDART00000046066:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.365
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(9.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(8.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTACAGGGGGCGGATG
R:
CAAAACTCTCCATCCTCCATTTGT
Band lengths:
159-234
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]