HsaINT0025358 @ hg19
Intron Retention
Gene
ENSG00000186193 | C9orf140
Description
suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]
Coordinates
chr9:139956579-139959431:-
Coord C1 exon
chr9:139959315-139959431
Coord A exon
chr9:139959240-139959314
Coord C2 exon
chr9:139956579-139959239
Length
75 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CCAACTGTGCACCTGCCCAGGAG
3' ss Score
3.79
Exon sequences
Seq C1 exon
GCCCTGCCCCCGTCCTCCTCCGGGCCCCCCTGCCCTGCCCTGACGTCCACCTCACCCCCGGTCTGGCAGCAGCAGACCATCCTCATGCTGAAGGAGCAGAACCGACTCCTCACCCAG
Seq A exon
GTAGGGCAGGCGCGGGAGGGGTGCAGGGGTGGGGGTGAGGCCCCGCAGGCCTTGACCAACTGTGCACCTGCCCAG
Seq C2 exon
GAGGTGACCGAGAAGAGTGAGCGCATCACGCAGCTGGAGCAGGAGAAGTCGGCGCTCATTAAGCAGCTGTTTGAGGCCCGCGCCCTGAGCCAGCAGGACGGGGGACCTCTGGATTCCACCTTCATCTAGTCCTTGTGGGCCGCGTGGGCCCCCAGGGCCAGCCTGGCACTCAGCCCTTCGAGGGTGGGCGCCCCATCGCACCCACCCTCTCTGGCTGGAGACCCCCGGCAGGCCCAGGCACAGTCCCGGAGTGGGCGCCTTCCTGCCGCCCTTGCCAGATGGGCTCCCCAGGCCTGCCCCCGGCTGGTCCCCGCACCGAGCGCTTGACTCCGTTTTGGCTCCTGGTGCTGACATGGGCTGGGGCTCTCTTGAGTCCGCATAGTCCGCAGCTACTACTGCCGCTGTCAGTGGACAGTGGGGTACCCCTCCATGAGTTAGCGTCCCCCCGTTTCCAGCGGTGCCGCCCTGGGTCCCATCTTCAGGGAAAGGCACTGCCCACGCCAGGCTGCACTTCCAACAACGGGCAGCAGAGGGCGCGGGGCGGCTCCGACGCGGGTCCAAGGGCAGCTTCCCGCTCAACCAGGGCACCAGGACGAGGTGGCTGTAGCTCGGACGGACGGAAGTAGATGGAGGGGGTGGGGACGGCCTGTAAGCGGGGGGTGCCTGCCTGGCTGGGGAGCCCCAGGGATAGCGGTCGGACTTCAGGTTCTGGCCAAGGCTGAGGGACCCTGGCTGCAGCGGATCGGCACGCCGGGTGGGCGAGAGCTTGGCCTGCATGTGCCTCCCACAGACCCTGGGGTGATGGCCTTCCCCCTCTTGGCCGGGACGTTGCCCCACGTTGAGTCCCACACAACATCCTGTGAGCCTGGCTCCCCAGGAGGGCCCCCAGACAGCTCCCAGGCACGTCATAGGCAAAGCCTGTTCCCCCGACTCAGGATTTCCAAGGCCTGGGGTCCTGCTCACCCCCCTTTGCTCTCACGCCCAGCCTGTCCCCAGGTTTCAGCTGGGAGAGGCCACCTCCCTCAGCCAAGGAAAACGAGAACCCCCAGGGTACAGGAGGAGGCTGGGGCAGGTCCCCTTGGGTGTCACTCCCTCAGCCCCTGCCCAGGCCCACTCCCGCTGGTGCTGGAGTACGCACTGGTGGGGGGGCCCTGCTCAGCCCAACCTGGAGGGTCCCAGTGTCACCAGAACCAGGGGCACGGCAACAGCATCGATGGGTTCTGCAGCCCAGGGCCCCCGATGCGGGGTCAGTGCGTGGGGGGCGCAGGGCCCCCGATGCCGATGCGGGGTCAGTGTGTGTGGGGCGCAGGGCCTCCGATGCGGGGTCAGTGCGTGGGGGGCGCAGGGCCCCCTCGTGTCCAGGGCACTTTGGTACACTGTCCCACAAGGCACCTGTCTCAGAGGAGGGGCCCTGGCAGGCAGCGTGGCAACTCCCTTCCGGAGCCCAGCTCCATGCTAACCTGCCCACAGCAACCCCACAGAGCCACATTCCCTGCTGCACCTGGTCTGCAGGGGTGTCCCAGGACAGGCCCAAGTCAGCCCAGCATGCAGCTGCCCTCCTACCCTGAAGATGGGAGTGGGCTTTCCAGGGGACATAAGGATGTCAGGCCTGGACCTCCTGGGCAGGAAAGGGTGCAGGTCCTGAGGGCCTGTGCCCCACAGCCCCAGCACCAGGTGGACTGCAGCGCAGTGGGTGGGCCAGTGGCAGCCAGGGAGAAGCCCCCCGTCAGCAGGCTGGGGTCTGCCCACCAGGGCCTCCCCACGTCTGCCTTTGAGGGTGCCTGCCATGCCCTGGGGGATCCTGGCATCTTTACTGGACTGGAAGCAGGAGACAGAACAGTGTCTGTCCCGGGGTGACTTCATCAGGAGACCGCCCACATAGAGCTGGACCCCGCAGCTGAAGCGGAAATGTGAGACAGGCTGGCACCTCCGGAAAAACTGCCTTTCAGCCTTGGTGTTCCGTGCAAGGTGAAAAGAAATAGGTCCTCCCAGTTTACAGCTTGAAATCAGGCTAGTGAGTGGCCCTGGAGACCACGAGGGGAGAATTTAAAGGCCCCGGCTGGCAGGGTCTAGGTGGCTGGCAGAGGCACATGCAGACCCTGCCTGGAGCCTGCCCTAGGACGCTGGGCGGGTCAGTCTCCGTGCAGGATGTGAGCAGCGTCCCTGGGCTCTATCCGCGAGGTGCCAGTAGCGTGTGCAGGTACATACACGTGCGTGCACACTGTGATGACACCCGGAAATGTCTCAGGATGTTGAAATGTGTCCTTGGGGGCAGAAGTGTCCCCAGTTGAGAATCTGCCCCAGAGGAACACACCCACACCAGGCCTCAGGATTTTGTGTTGATCAAGTTCCAAGGAAAAGGAACATCTCAGCCGGGCGTGGTGGTTCACGCCTGGAATCCCAGCACTTGAGGCCAGGAGTTCCAGAGCAGCCTGGGCAACGCAGTGAGAGACCCCATCTCTACAAAAAAAAAAAAGAAAGAAAGAAAATGAGAGATCCAGGTTTAAAAATTCATAAACACCACAAGGAAACAATACACTATGAGACCCAGCAGAAGCAACAGATTGACTCTAGACCCAGATACTAGAATTATCAGAGAGAATATAAAGTAACAGTGTTTTATATATCTAAAGAAATAAAAGAGATTTCTGGAAACATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000186193-C9orf140:NM_178448:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.513 A=NA C2=0.310
Domain overlap (PFAM):
C1:
PF097894=DUF2353=FE(24.1=100)
A:
NA
C2:
PF097894=DUF2353=PD(22.2=81.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCAGACCATCCTCATGCTG
R:
AAGGTGGAATCCAGAGGTCCC
Band lengths:
170-245
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)