RnoINT0029142 @ rn6
Intron Retention
Gene
ENSRNOG00000018480 | Capn9
Description
calpain 9 [Source:RGD Symbol;Acc:70965]
Coordinates
chr19:57377519-57378901:+
Coord C1 exon
chr19:57377519-57377577
Coord A exon
chr19:57377578-57378544
Coord C2 exon
chr19:57378545-57378901
Length
967 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
ATCTCTCTCTTTTCTTCCAGTTC
3' ss Score
11.39
Exon sequences
Seq C1 exon
GGGTGTTCCAGTGTCTCAGTGTGAAGAACAAGGACTTCATCCATCTCAACATAAACGAG
Seq A exon
GTATGGCCAAGCAGACCCCAACCAGGGCCTGGCAGAGTATGAACACTCTAAGTGGAGCCCCAGGCAGGGCGAGAGCTCGCTGTGGGCAATTACCCCGTGTGGAGGCCGGTGTTTCTGTCCACTTGGCAGTCAGCATAACCAGCGCTGTAATCCTGTGAACTGTGGGTGTCTCCATTGCCCTGGTGTCTGCTCATGCTAGCCCCAAGAAAGAGGGTGGGGAGGAAACAGAACGTTCCAGATAAACATGAGCAAACCCAGTGAGAAGAAGGGAGAAATGAGATGCCTGACCCCATCCCCACCTCCCTTCCCGTGGTAGAGGGTCAGCTTTCAGCTTTCTCTGAAAGGTGAATTGCCAAAAAGCAAGCCCAACTCACACTACCCTGCCCCAAGCTGTCTCTACAAGGCTGTCCCCTTCAACAGGGACAGAACACATTGTATCCCTCTGTCCTATCTGCCCTCTACTGAAAGTTCACTTAGCCTTCTCAAGGTTTATCTCATTGGGGAGATGTACCTGCTGCACAAGCGTGAGGACCCACGTTTGAACCTGCCCCATGGTCCCTGGGAAAAGCCACGTTTGGTGGCACTCCCTCCACATGGTATCTGGAATTCCAGCACTGTGTGGGGGTGAGGCAGGTGGATCTCTGAGGCTCGCTGGCTTCAGCCAGTGTGGTCCATTGGTGAGCTTCAATTTCAGTGAAGGACTGTCTCAAAATATAAAATGGGGAGAAGAACGCCCGATATCGAGCTCTGGTCTGCACCACACGCACATACGCATGCATGTAGTTATACACGAGACACACCCAGCAATCTGTTTTAATTTAAATTTTAAATAAATGGTTTCACGTTGAGTCAGAAGCCCAAATTTGTGCAAGATGACCAGCAGAGTTCTTGCGACACAGACAATCCCAGGCCACACCTCAGTTGCTGGGCTGGGTTTCCTAAGCCCCATCTCTCTCTTTTCTTCCAG
Seq C2 exon
TTCATCAACTTGACCATGAACATCTGAGCTTGCACTGACCTGATGCCGTCTGCCCCTCTGATACTCAGCTGCTGGACCATGAACCTCAGAATTTTTATTGGAGGGCCATCCCGCCCATTGCTCTCTCCCCACTCCACACCACCCTCCTTCCCTCCCTGTCGAGATTTAAATCAAAAAGGGATTGGCCATGTTCTCCGATTCAGTGATACTTCTTCTAAGATCATTGCTCCACAGGAACTCATGGCACTGCCTGTGTCTGTGCTCAGGCCTGGGGTTGCTGTATGCTCCTCCCTCCACTGCCCCTCCTCCACCAACCGGAGTCCTGGCTTCTGAGTGCTCCAATCATGCTATCAAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018480:ENSRNOT00000025357:19
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTGTTCCAGTGTCTCAGTG
R:
CAGTGGAGGGAGGAGCATACA
Band lengths:
358-1325
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]