DreINT0041101 @ danRer10
Intron Retention
Gene
ENSDARG00000052702 | capn1a
Description
calpain 1, (mu/I) large subunit a [Source:ZFIN;Acc:ZDB-GENE-040426-1263]
Coordinates
chr13:42555333-42556247:-
Coord C1 exon
chr13:42556189-42556247
Coord A exon
chr13:42556100-42556188
Coord C2 exon
chr13:42555333-42556099
Length
89 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCTC
5' ss Score
2.13
3' ss Seq
CCCTCTTTCTGTTTGCGTAGTGG
3' ss Score
7.61
Exon sequences
Seq C1 exon
GATCTTTTCAACAGCTGGACAGAGAAGAAACAGGAACGGCTGAGATGAACCTATCTGAG
Seq A exon
GTGCTCTGGCTTGATTTCTTTATATTTTAAATAACTAAACAAATGACATGTTCAAAAATACTCATCTCTCCCTCTTTCTGTTTGCGTAG
Seq C2 exon
TGGCTCTTCATGACCATGTGTGGTTGAGGTACAGCGTTTCACGAATGTCCAACACAAGAACCTGCTGCGAAGTGCCTCCTCATGCAACAATCCTGCTGTAACCTCACTACAACAAAGTGCTACTTTATTTAGACAAAAAATCATAGAACACATTGTAGCTACACTACAAGAAAACACACTAAGAGACAAAAGGATCTTCACTCAGCGCTTCAGTTATGACTGAAGGAACGGCTGAGGAACATCATGTGCATGGGATTAATATCAAGTGAGCTTCATGTTTTGCATTTGTCCTTTAAGACCAATATTCAGTTCCAAAAGGTTGAATTCTGATAGTGCCATATGAAAGAAACTGCATGTTCATCTAAAGGTGAATAATGCATCCCAGTTAAAGCTTTAGATGCACAATGCGGGAATGCGTAGATATTATTAATGACCAGAGCTTCAGAATAAACTTATTTTAACATGCGTAAGAAACGTTTTTATTTCATATTATGCTCTGAGAATATGTCTTCCTAAACATATTGGTGTAGAATTAAACTAGCATTTGATTGGATTAATGGTATACTACACAATTTAGCCACATATGTGTACAGAACAAGTACTGTGTTGTTTTAATCCACATTACATGTAGATTTTAAATGGAAGCGTCTACTTTTATATACTTTAATTTGAGCCAATCAGTATTGATTCTGATGCCAAGAACAATCTTTCATTCTGTGCTGTTCAGTTGATGCATGAATAAAGCTCCACTACACTTATTGCACCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052702:ENSDART00000046066:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAACAGCTGGACAGAGAAGA
R:
TGTTGTAGTGAGGTTACAGCAGG
Band lengths:
167-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]