HsaINT0027550 @ hg19
Intron Retention
Gene
ENSG00000135773 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:1486]
Coordinates
chr1:230910300-230914879:+
Coord C1 exon
chr1:230910300-230910377
Coord A exon
chr1:230910378-230914718
Coord C2 exon
chr1:230914719-230914879
Length
4341 bp
Sequences
Splice sites
5' ss Seq
CTGGTACCG
5' ss Score
4.81
3' ss Seq
GTCTCTCCGCTTTGCTGCAGGAT
3' ss Score
9.29
Exon sequences
Seq C1 exon
TTCTCCGGAGTGGCGTTCTGTTGGTCCAGCTGAGCAGAAGCGTCTGTGTCACACTGCTCTGGATGATGGGGAATTCTG
Seq A exon
GTACCGTGCTTGTTCCTGTGTTAACTGCAGATACGAGCAAGTCCCATGGCCCTGGGGCGTAAGGAGCACTGTGCTTCTCTCTCGCTTTCCTTTTTCTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTGAGACGGAGTTTTGTTCTTATTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCGTCTCACTGCAACCTCTGCCTCCCAGGTTCAAGTGATACTCCTGCCTCAGCCTCCCAAGCAGCTGAGAGTACAGGCATGCGCCACCACGCCCGACTCATTTTGTATCTTTAGTAGAGATGGGGTTTCACCGTGTTGGCCAGGCTAGTCTCGAACCCCTGACCTCAGAGAAACCACCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGTATGAGCCACCACGCCCAGCCTTCTCTCTCCATTTTTGGCAAATCAAATTCATCTGTCTCAGACTCCTCATATACACCCAGATTAGAGGGAAATTTAATCTCCCTCCTGTCTTGGTGGGGGCTCACCCCAGCTCTCGGTTTGTTGAAGAGTCTTCAGGGGGTTCCTGCAATCCAATAGAGGAAGAGCCTCTGGTCTCTAGCCTGACACACCTCCTTGGCACTCTTTGTCATCCAGGTTTACACAGTGAATTTGAAGACAGGCAGCCCTACTGCTCACAGGATCCATTCCCTCCACACCCATCTTGATGAGAGGTACCTTTGAAGGCAGCTGCCCTGAGAGCATCTAAAGATATCGACCTACGTAGGAAGTAAACATTTCTACTCTGGACTTTCCCTTGGCCTGAATCTCTTTGTTTAATTGAACATTTGTATTGGGCCTTCATCTCTAGAATCTTTTTCAGTCTTATTTCTTCCTGTTTGGGTTCTAGAAGTTGGCCCTTCTAACCCTGTGAGACCACAAATTTCTGGTTTCTGGCTCTATTCCCTTTCATGTGCTCCAACCAATCAAGTCTTGCCTGAGCTCATCTCTTTCTTGTAACAGCTTTTAAAATACAACAGCAGGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGTGGATCACGAGGTCAGGAGATTGAAACCATCCTGGCTAACACAGTGAAACCCCACCCCTGCTAAAAATACAAAAAATTAGCCAGGGGTGGTGGTGAGTGCCTATAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGGTGGAGCTTGCAGTGAGCCGAGATTGCATCACTGCACTCTAGCCTGGACAACAGAGTGATACTCCATCTCAAAAAAAAAAAAAAAAAATACTACAACCCAAAACCATGACTATTCCAGCCTTTTTCATTCTTTTCCCATAGAACACAGCCTCAGTAGTGATTTGTTCTGCCTTCTGTATTTTTATAGTTGTCTTAGTCTATTTGGGTGGCTATAAAAAAATACCATAGACTGAGTGGCTTACAAAGAACAGGAATTTATTTCTCACAGTTCTAGATACCAGGAAGTCCAAGAAGATGACACAGGCAGTACCTATATCTGTGGAGGGCCCTGTTTCTGATTTATAGATGGATCCTTCTCACTCTGTCCTCACATGGTAGAAAGAGGGCAAGGCAGCTCTCTGGGGCCTCTTTTATAATGGCACTAACCCCATCCATGAGGGCTCCACCCTCACAACCTAGTCACCTCCCAAAGGCCCCACCTCCTGACACTACTACTTCGAGGGTTAGGATTCAACATATGAATTTAGGGGAGACCACAAACATTCAGTCCATAACAACATGCAACAGATTTACCCAATGTTTTGCCACTGCATAACATAGATAACCATTTTCCAGCTCGAACAGTTCCATGATCCCTCTTGCTCAACTGCTAACATATTTTAGAATTTCGTTGTGGCAGTTCTGTAATTCAAGGCACCAATGACTCAAGGTAACACTAGCTGCAGTAGTGAATAGACCCCAAATATATAAAGGCTCAAACACAGTAAAGTTTTTTCCTCACTCATTATGACAGTCCAGGGAGGATGTTCATATTCTGTGGGTGGCTCTGTTCATACAGTGATTCAGGAACCCAAACGCCTTCTATTGTGTGGCTCTGCCATCTTCTAAGGTCACGTCATCATCTGCACATAGCCAGCAGAAGAGAAGAATAAAATAAAACATTGAAAAAGACACTCTCACTTTCTAAAAATCTTGACTCAGAAGTAAATGCGTCACGGCTCACATTCTACTCCCAAATGGAAGGAGTGGGGTGCAGTCTTGGTCCTGTGCTGATGACTGCCAGCCATCTCTGCCTCGGGAACCATGAGGGTTTAGGTTCCCCAGATTTGTGGAACACATGCAGGGTGCTTGAGAGATTCCCAAGCTGTCAAATTAGAAATTACAGATAAACTTTGAATTTTGAAGTACAGGGGACTTTGAGTTAGGGGGTTACAAGAGAGGAGCAAAAACTGCAGGAAGAAAGCTGAGTTCTGGAATTAGTACCATCACAGTAATTGCTGCATATGAGCAGGAGGTAGAAACCAGAGTTTGAGAGGCTACCTGAGGTCAGGCTAGTGGAAAGAAGGTCTGGTGCAGACGGTGGGAGAAGCCGGGCAGAGGAAACTCGGAAATTCACAGCAGGAAGCTCCACAAAGAAGAGCGTCCATGTGAGTGATCCATTGCCCTGCCCCTCTTGAAGGAGCAGCCCCAACACCAGGGCTGAGCCTGCCCAAGGTGATGGGTGGTGTTAAATCATGCACTCTGTGCGTGGAGCCCTTCCTCCTGGAATCCTGACTCTGAAGCCCTGTGTAGCCTCTTTCCATTCTTCACCAGCTCTAGGATGTACCTCCTGCAACTCTCTTCTCTCCCCTTACGTATGAATTCCCCCCTTCTTCTGAATCATTCCCCTTAGCACTCCAACACTATCATTTCTCCTACCTGCAAAGAAAAAAAAAGCCTCTCTTGACCCACTCAAGTGACCAACCCAGCTCTCTCCTGTCCTCTACAGCAAGCCCGCCAGTTCCTCTTCTCCCTTACTCTCTCGACTCCACTCAGCTATGAGTGTGCCCCACCACCCCACTAACCCTGATCTTGCCAGGGACGCCACCGACTCTCACTTTGCTCGATCAGATTATCTTGATCCATCAGGAGCCCTTGACGTGCTGGATTGCGGGGGACCACACGCCCTGGTGGTCCTCCTCCTACCTGAGCTCCTTCTCAACATCCTGTCCTGGCCCCCTCTCATCTCCCTAACCTGTTAGCACTGAGGTGTCCCAGGACCCCATCCATGGTCCCCCTCCTGGCTGTCTATTCCCACTCTTTAGGCGTCTCGTCTGGTCTCTTGACTTTAAAAACTATCTTTACACTAATTCTCAGGTTTCTATCTTCAGCTCCTTTCCCCAGGATTCCAGAGTCACATATTCAATGGTCTACTTTAACATCTCTCCTTGAATGTATAATAGACATCTCACATTCACGTGCCCAAACCTGACCTCCTGAGCTTCTCTCTCAAACTGCCCCACCACAGCCTTCCCCATCTCCATCCTTCCAGTCACTCAAATCAAACATCCTGATTCCTTTCATTCGCTCCTTCCCCACATCCAGTCCATTAGCAAATCCTATAAAATTTACCTTTGGAATGTGTCTCAAATCTGGCCACTGTTCATCACCTCCCATACCATCAGCCTGGACCAAGCCACCCTTGTCTCTCACTTGGACACCGGCACTAACTTCCTAGCTGCCTCTCTGCTTCCACTTGTGTCCCCAAAATCTGTTCTCAACACAGCAGCCATGGAGCATGTGACTCCTCTGTTTACTGCCTTCTAAAAGCTCTCCATCTTCTCAGAGTCAAAGCCAAAATCCCTATACCTATTTGATGTACTATGATCTCTTGATCTTATTCCTTACAGACACCTCGTGCCTTCCTGGTGTTCTGTGAGCACCTCAAGCACCTCTCTGCCTCGGGGCCTTGCTGTCCATCTGCCTAGACCCCCAGAGAGCTGCCCTGCCCAGGACCTGGTAGTTCAGGTCTCCACTCAGAATGTGCCCCATCAGTAAGGGCTTCTCTTACCTCCCTGTTTAAAATAGCATCCCACCCCTACGCTCCCATCCTTCAGCCCAATTTGGTTTTTCTCTGTAGCACTTAACATCTACAATCAATCTATATTTTTAGCCTGGTTTTTACCTTTTTAACCTTTATTTTACTTTTAAAAAATTTTCCATCTCCCCACACTTTGCAGTCCCCCCACTCCTTGCGGACAGGAACAAGATGATTTAATGAATAAGTGAATGATTTAATGAATGAGTGAATGGATGATGCCCTCACTCTTGCCCTCCTGTGCATCGTGTCTCTCCGCTTTGCTGCAG
Seq C2 exon
GATGGCATTTAAGGACTTCAAGGCCCACTTTGATAAAGTGGAGATCTGCAACCTCACTCCCGATGCCCTGGAGGAAGACGCGATCCACAAATGGGAGGTGACGGTCCATCAGGGAAGCTGGGTTCGCGGCTCCACGGCTGGGGGCTGCCGCAATTTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135773-CAPN9:NM_006615:8
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.123 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(12.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)