DreINT0041110 @ danRer10
Intron Retention
Gene
ENSDARG00000052748 | capn1b
Description
calpain 1, (mu/I) large subunit b [Source:ZFIN;Acc:ZDB-GENE-060503-491]
Coordinates
chr22:26287697-26289324:-
Coord C1 exon
chr22:26289155-26289324
Coord A exon
chr22:26287909-26289154
Coord C2 exon
chr22:26287697-26287908
Length
1246 bp
Sequences
Splice sites
5' ss Seq
GAGGTTGGA
5' ss Score
2.95
3' ss Seq
TACTTTTCTTCTGTTTTTAGTTT
3' ss Score
9.39
Exon sequences
Seq C1 exon
ACACATTCTGGATAAACCCTCAATATAAGATCACACTACTGGAGGAAGATGATGATCCTGAGGACAATGAGGTGGCCTGCACCTTCATGGTGGCTTTGATGCAGAAGGACAGACGGCGTTTCCGCAAGCAGGGACAGGACATGCACACCATCGGCTTCGCCTTATATGAG
Seq A exon
GTTGGAGGTCATAAGCTGACATAGAACAGTCACACACATTTAAAAGTACCATGATTTTGTCTAATTTATTTATTCCTGTTTTTTCTCATTTCTAGGTCCCAGATGAGGTATGGCACGTTTAACACTATATGAATCGAAAGTTTGAAATTCAAATTAAAAAAATTGTATGTAAAATGCTGAGGCGTCATTCAGATATGTGTAAACAGGACGTTTCGGAGACTTTTATTTCAGTGTATTGATGTACTTCAAACTGAAATGGAATATTGAGTAGTGGCGGGCATTTCTTTTTCGCATAATTCGCTTGTTGCAAACTAATGGCATTAGGGGCATGGTTAAGAATATGGACTCACCATGTGGTTAGGCAGTGTTGTCAACTTGGATTTAGCTAAAAAAAAATTCAAAAAGCACCTAGCAACAAATTCTGCAATTTTTAACATTTGCTTTTAAAAAGTGTCTCAAATCAAAAGTGCAGTTGTGACCAAATACTGGTCTAAATAGCTGGGCACAGAAGATGCAGCAGCAGCCAATAGTATGTTTCTGCACAACCAGAGAGGATGGAAGGTATTTTAAGATCCTGTTGTTCCTGACCTGTTCAGTAAAGGGTTTAGGGGTAGGGCCATAATAAATCCTAAAAATGCAGTCATGAAACTGTAGTCTCTCTTTTTATGCTAGAACACCAGCAGTATTTGTTGGCCTGCATATTTTTGGTGAAATAAATAAAACCATAACTAAACAATTGTTTGATGCAACAGTTGTCAATTTGTCACTAACATGTATAATTGTTGTTCATTTAGGTAGCACTAACTACCAATACAGTGCTCTAACTGAACATTCACATAATGTTTCTGCTGAAAGGCCATTCTTTGAGAAAACTCATTTATTATTTTGCACACTACATAAAGATGCAGTTTTGTGTTGTGATTACACAATGACGTCATCATACAATGATATCACGTCATTTAACAACTTTTAGTAACACATTGCTTCACCTTTTGCAAATTCAAAACCAGTAGTTGGCAACAGTGTGATTGGGATTAGAAGGTAAGTTAGGTTAAGGTTAATTATGCAAAAATAAATTTTAATTACTATAGTACATACATGGAACATGTAACAAGGGCACTTTAAAATGAAGTGTTACCCAATTATTTTTCAAATCTGTTTGGTGATGCAGCAGTTTTATTTTTGAATGTATTGTAAAACATGAGGTTAATAATTTAAAAAACTTTTACTTTTCTTCTGTTTTTAG
Seq C2 exon
TTTCTTGGCTCCCAGAATGTTCACCTGAAGAAGGATTTTTTCTTGCGTCACTCGTCCTGTGCACGCTCCGAGACCTTTATTAATCTGCGAGAGGTGAGCACGCGACTGAGGCTGCCACCGGGCGAGTATCTCATTGTCCCTTCCACTTTTGAGCCTGGAAAAGAGGCTGACTTCGTCCTGCGAGTATTCACTGAGAAACAGTCAGAAACTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052748:ENSDART00000105099:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.035 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(36.8=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(46.1=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACATTCTGGATAAACCCTCA
R:
CGAAGTCAGCCTCTTTTCCAGG
Band lengths:
345-1591
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]