DreINT0041164 @ danRer10
Intron Retention
Gene
ENSDARG00000055592 | capn2b
Description
calpain 2, (m/II) large subunit b [Source:ZFIN;Acc:ZDB-GENE-050522-84]
Coordinates
chr22:26317204-26318542:-
Coord C1 exon
chr22:26318382-26318542
Coord A exon
chr22:26317368-26318381
Coord C2 exon
chr22:26317204-26317367
Length
1014 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGC
5' ss Score
5.03
3' ss Seq
GTTCATTTAATGCTCTACAGACA
3' ss Score
5.26
Exon sequences
Seq C1 exon
GATGGCATTCTCCGAATTCCTCACCAATTACTCTCGTATAGAGATCTGCACTCTGACGCCGGATGCCATCACAGATGATTCAGTAAAACATTGGGCCGTGACAAATCATGACGGCACATGGAGGAGAGGCTCCACCGCTGGAGGCTGCAGAAACAATCCAT
Seq A exon
GTGAGCCATAAAAAGCATTAACTCTCCAAATTAACCAAGAGTTGTGGATCAGGGACAAAACATTTTCTCACTACTAATTCAGTTCAATTCATCTTTTATGTCTATGCCGCTACAATGTAGATTGAGTCAAAGCAGTAGTGATGGGAGGTTCGGATCATTTTACTGACTCGGATCTTTGAGTCTCGTTCATCTAGATCAGGGGTGTCAAACTCAATTCCTGGAATGCCGAAGCCCTGCACAGTTTAGTTCCAACCCTGCTCCAACACACCTACCTGTAGGTTTCAAACAAGCCTGAAGGACTCAATTAGTTTGATCAGGTGTGTTTAATTAGGGTTGGAACTAAACTGTGCAGAGCTGCGGCCCTTTTGGAACTGAGTTTGACACCTGTGAACTAGATAAACAAATCTTTTTTCGAGTCATCTCTTTAATTTGGTTCAATTTGCCAAAATATTATTAAAATGTTACGAATTGCTTCCAAACACATCTACAACTAGCCCAAAATGTTGATCACATAACAAATAAGTCATAAATAGAATACTATAAGAAGGAGAAAATAATAATTCAATGTTTACCTGTTCTTTTGTCTATGAAGCTCACCTCTTCATGTCTTCAAATGTCAGTGGTTCGTTTACGTTACTCTGACAGTCGCATATAATCTTAACCAATGTACATAGTCTGAGCCGATAGGAGCCATGATAAATAGTTCACCTGTCGAGTCTTTTGGTTCTTGAGTCGTTCGTTCATCACATGACAGAATGACTCAAACCCGAGGACTCGAGAGATGAACGGATCAATTCTTTTTCCGGCTCTAAACGCAAAGGATTAGCTTCTGCCTTTCCGCTATGAACGACTCAAAAGACTTGAAATGAACGATACCATAATTAACACTTCTTGTATGTATTGCCTCTTATTGAATCGCCACTTAAATTTTAGTCGCTTTGGACAAAAGCGTCTGCTAAATGATTGAATGTAAATGTAAAAATTTTGCTGACCGGTTCATTTAATGCTCTACAG
Seq C2 exon
ACACATTTTGGATGAATCCACAATTTGTGGTGAAACTGGATGAAGAAAATGTCGAAGATAAGGAGAAGGGCTGCAGTTTTGTAGTGGGTCTGATTCAGAAGAACCGCCGGCGCCTGAGGAAAACTGGAGAGGATATGAACACTATTGGCTTTGCTATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055592:ENSDART00000077958:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.091 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.4=34.5),PF0106717=Calpain_III=PU(15.6=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCATTCTCCGAATTCCTCAC
R:
AAATAGCAAAGCCAATAGTGTTCA
Band lengths:
318-1332
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]