HsaINT0025354 @ hg19
Intron Retention
Gene
ENSG00000186193 | C9orf140
Description
suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]
Coordinates
chr9:139960714-139965028:-
Coord C1 exon
chr9:139964342-139965028
Coord A exon
chr9:139960827-139964341
Coord C2 exon
chr9:139960714-139960826
Length
3515 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCATGCCTCTCCATAACAGGTG
3' ss Score
9.24
Exon sequences
Seq C1 exon
GCCCCATTCAAAAGTAGTCGCTATTGTCGCCGTGGGCTGAGCTCGCCGGGCCGGCCCCTCCGTGGGGCCGCGCTGGGACGCACGCGGGTGGACGAGGGGACCGATCCCGGGCGCCCATGGCCGGGGCCGCCATGGCCGAGCGGGGCCGCGTGCCTCCCCCCGCACCCGCGCCCAGCACGGAGGGGCTGCCGCGCGCCTTCCTGCAGAGCCTGCGCACCCTGTTCGACATCCTGGACGACCGGCGGCGCGGCTGCGTGCACCTGCGCGAGATCGAGTCCCGCTGGCAGGGCACCGACGCGCGGGAGCTGCCCCGCGGGGTGCTGGAGGGCTTGCGCCAGGTGGCCCCGGCCAGCGGCTACCTGACCTTCGAGCGCTTCGTGGCCGGCCTGCGCACCTCCCTGCTGAGCGCCGACGGCGGCCCCCGGGACCCCACGCGCGCCCCGGCCCGGCCCGGGGATCAGCCGCCGCCGCCGCCGCAGCGCCTGGTGTTCGCTCCGGCCGACGAGCCGCGGACGGTCCTGGAGAGGAAGCCCCTGCCCCTGGGCGTGCGCGCCCCTCTGGCCGGTCCCAGCGCCGCCGCCCGCAGCCCGGAGCAGCTGTGCGCCCCGGCTGAGGCGGCGCCCTGCCCCGCGGAGCCCGAGCGGTCCCAGAGCGCGGCGCTGGAACCGAGCTCCAGCGCGGACGCAG
Seq A exon
GTGAGTTCCGGACGGCCCCCGGGCACCCTCGTAGCTCTCCCGGGCCCGGGCCAGAAACCGCAGTCCCACAGCTGCTGCCCGTGCATTTCCCACAAGGGACGGGACCGGGGAGCGGCTCTTCGTGGACTCCGGATCCTGGAGGGCGCCTCGGCGGGTCTGGAGGGAAAGGGCTTCATGCTTGTCGCGGTGAGCCCAGGGGCTTGCTTAGGGAGGCAAGCCAGACCCTCTCCTGCCACAGCATAAGGCCACCAGGGCCGGGGGGTGGCAGGTGACTCAGAAAACCCACCGGGAGCCCAACCTGTACCAAGCCTGAGCTTGGGCTCTCCATCTCCAATACCCTTTCCGCACCTGGGGACACCTGGGCCCTCAGCCTCCTGTCTGTGGCTGCTCAGGCAGAAGTGCTTCCTTCTCAAAGAAAGGGTCCCCCTTCTCAGTGTGACAGCTTAGCCAGGGGGGCTGGGCCCACTGACCCCACTGAGGCCTAGGCAGGCGGGGGCTGCTGCTGGTGGCCCAAGAGGACCTGGCCCTGTTGCCAAGATGGGCAGGGGCGTGGGTGGATCTCCTGCACCCCAGTGGGGCTGTACTATGGCAGATGCCATGGAGGGACATAGGCCGTAGTCCCTGGGGATGGCTGGCACACTCCTCTCCTGCCTTCCGGTCCAGTTGGCAGTGATGGGAGATTGCTGAATGGTCCCCTGTCTCCCCCAACCCAGTGCCTGCCTTGGGAACAGGACCTGTATTATGGCTGGGGTTGGGGGGCCAAGCTCCCAGAGGGGCCCCAGGCCCCACAGCCCATTCGGCCTGTGCACCCGTTCTGCCAGGGGAGGCCTGCCCACCGGTGGCTCCTGCCGGTCCCTGTGCTGCCTGCTGCTCTGCCACCCTCCCTGTACTGCTCCCCCACCTCAGCCATATTCTCCAGCCCTACAGCTGGTGTTTGGAGCCACGGCGGCCCTGGCCTCCCTGGTGATCTGATCCAGCAGCCACACCAGGCTGGGGGACCCCTAGTTCTATGGTGAGGGAACCTTCAGAGGGTATCTGGCTCCAAATGCAGGGTCAGCGTCATCCATGTGGCCATGCAGTTTGAAATCAGCCATGGGATTGCACGCTGTGGCCGGGCCTGGGGTTTGGAGGCCTAAGCCTGTGGTCCACCCCTGCTCTGCTCTGATGCCCCATGCGGCACTGGCTCACGTACCACATCTCCCTGAAGGCCACATGGCTAGGGCTGTAGCTGTCACCCTCTCACAGGCAAACGGAGGGCCAGACAAATGGCGTGACATATTTGATTGACACAGCTGGCTTTTGGGGTGTCAAATCTGGAGCTCTGAGGTCACCCCAACTCCCAGAAAGCCTGCCAACACACACAGCCTTCCAAGCCCCCAGCCCAGATGTTCAGGGCCTCTTTCCTTGTTCCCACCTGGGACTGCGTGTTTGCTCCAGGCTGGCTGTGGCCCTGGAGGTGTGGCCTGCTGGCTCAGGGCCCTGGAGGGGCAGAGCCACCACCCCCACCTAGAGGCCATCTAGCTCATCACCCAGCACGCTGCTATCTGGGGACCCAGGAGCTGCTCTATGGACTCAACTGTACAGACCGGGCCCAGGTGTCCTGGGACTTCCTCTATGGCCTCCCTCTGTCTGTACCCTCTCTGCTCCCACCTCCTGAAGGGCTGTGTGCTCTTCCACTGTCTTGCCCCAGAGCTGCCAGCCGCTCAGCACCGCAGGCTGGAGTGCGAATTCGGGCCTGCCTGGAGCCAGGCTCTCTGCCGTGCCTACCTGGGCCCAATTCTTGCATCACTCCCTGACTCCTGTGGCCAGGTGCCAGGGGCATGGCCTCTAAGGATGTGCCTGGTGCTGGGGCTACAGCTGGAGGCCGAAGGAGGATGCCTTCCTCCACACCTGTACCCACTTCTGTAGCCTGGGGAGGTGCACCTACTCCCTCACCAGGAAGCTGGGCCGGAGTGGCACCAACGCGATACTCTTGGCTGCCCCCAGGGGGAGCCCTCAAACAAACTTCAGAGCAGGGGTCTGTGAGCACCAGGACGTGCCTGACTTGTCAGTTGGGTGCACCGCCTGGCGTATCACACACGCGGGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGAATCTCAGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCGATCCTCCTGCTTCAGCCTCCCGAGTAGCTGGGATTACAGGTGCATGCCACCACGCCCTGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCTAGGCTGGTCTTGAACTCCTGACCTCAACTGATCCCCCCCCGCCCCAGCTTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCGGCAAGGGATCTTTTTTTTTTTTGAGACAAAGTTTTGCTGTGTTGCCCAGCCTGGAGTGCAGTGGCGCAATCTGGGCTCAGTGGAACCTCTGCCTCCCAGGCTCAAGCAATCCTCCTGCCTCAGGCTCCTGAGTAGCCGGGACCACAGGTGCATGCCACTGCACCAGGCTAATTTTTGTGTTTCTAATAGAAATGGGGTATTGCCGGCCGGGCACAGTGGCTCACGCCTGTAATTCCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCAGGACCAGCCTGGTCAACATGGTGAAACCTCATCTCTACTAAAAAATACAAAAAGTAGCTGGGCATGGTAGTGGGTGTCTGTAATCCCAGCTACTCGGGAGGCTGAGACCGGAGAATCACTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGATCATACCATTGCACTCCAGCCTGGGCAACAGGAACAAAACAACGTCTCAAGAAAAAAAGGAAGAAATGGGGTTTTGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGAGCTCAAGCGATCCACCCGCCTTGGTCCCCAAAAGTGCTGGGATTACAGGCGTGAGCCACTGTGCCCGGCCATGCGGGACTAACTTTCTATCAGAGTCACCATCCTGGGAAAAGTTAGGTTTCCGTCATTCACACCCACATCTCCTGCTGCCTTGCAGGACCCCGTGCAGATGGGAGAGGCGTAGTCAGGACCAGAACCCCCCCGCCCACTCCTCCCTTACCCAGCTGCCTTGGAGACCCAGGGTGTGCCTGCCATGTTCTGGGCACTGGGTGTGCAGAAGAGAGCTGGATAAGGCCTCTGGCCCCAGAGAGCTCACGGACCGATGAGGGGGCAGGGTGTGTGTTTGAGCAAACATGCGGGCTTGGCGGCACAGCCCTCCCCAAGCCAGTGTGAGGAGCTGGAAAGGGGAGAGGGACCAAACTCCAGCCTGGCACAGAGGCTACACGTGGGCCATGCCAGGCTGGTGCCCGAGACCTCGAGGGTGGGCTGAGATGTGGAGGCCGCTGCACCTCAGCAGAGCCTGGCCAGGCAGGTCTGGAGGTGAGCCAGGCCCATGCCTCTCCATAACAG
Seq C2 exon
GTGCAGTGGCGTGCAGGGCCCTGGAGGCGGACTCAGGGGATGCCCGGCGGGCTCCCCGTGCCCGAGGGGAACGTCGGAGGCACACCATCGCCAGCGGCGTGGACTGCGGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000186193-C9orf140:NM_178448:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.716 A=NA C2=0.667
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF114143=Suppressor_APC=PU(4.8=10.5)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)