HsaINT0042117 @ hg19
Intron Retention
Gene
ENSG00000183117 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:14026]
Coordinates
chr8:2966125-2967857:-
Coord C1 exon
chr8:2967680-2967857
Coord A exon
chr8:2966271-2967679
Coord C2 exon
chr8:2966125-2966270
Length
1409 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGA
5' ss Score
5.24
3' ss Seq
CCTCTTTCTGTCTTTCCTAGGGA
3' ss Score
12.32
Exon sequences
Seq C1 exon
CCCCTTGTGGGTACAACGTAACTTCTCAGAACGGCACCATCTACTCCCCTGGCTTTCCTGATGAGTATCCGATCCTGAAGGACTGCATTTGGCTCATCACGGTGCCTCCAGGGCACGGAGTTTACATCAACTTCACCCTGTTACAGACGGAAGCTGTCAACGATTACATTGCTGTTTG
Seq A exon
GTATGAGAACCTCTCAAGTCAAAATATCTGTAATTGTGATCAACAATTCTGACTTAGCATACATATGCCACTTATATACAAGGCACATATTTAGAATAAACTTCTTAGATACTAGAGAAGAAATTCACCAACGAAATCCAGAGATATAGGGAATCAATTTCACATAGTACATGTGGGTTTTGCTACATGGTAGAAATAGGCAGAATTATGTCTGTGTGTCTGCATCTGTGTGTGTATGTATTGGATGTGTGTTTGTGGGTGTGGGTTGGGTTGGGTATGGGTGTGTGATGTGTGTCTCTGTGGGTGTGTCTGTGTGGTGTGTGTGGCTTGTGTATGTCTGTGTGGCTTACGTGTGTGTTTGTGTGTGTGGTGTCTGTGTGTGTGTTGTGTATGTTGTGTGTGTGTGTGCGTGTTGTGTGTGGTGTGGCTGCACTCTTGTTGGAGCCCACAGGGGGAGCAGGAGCAGAAGCCAGCAGCCAGGGCAAGTAAGGCAGGACCTGGAAATGCATGTGAAGGCCTTGGGCTTTGTTCTTGGGGCAGTGAGGATGCACCTGGGCTCTGACAGGCAGAGCTCCAAGGCCAGATATGGGCTGCAGAATGACGGGCTCATTTTGTGGGAAATAAAGTAGCAGAGGGCAAGAAAGGAGACTGGCTTTGAGGTTGTGGAAGTAAATCAGACATCTAAGATGACAACGACCAGAGTCAGTGGATGTGAGAGTGAGGAGAAACAGAATTTGAAATATTAGGTTGACCACAATGAAACTGCCGTTTTAAAACCAAAACAAAACAGCATTCTGTGGTTGGCCATGCCCCATAGATTAAGCTCCATATTTAGAATGGAAAATCTCACAGGTGTTGACATTTTTATTTTATTTTTTTAATTTATTTCTTTTTGAGACAGAGTCTTGCCCTGTCGCACAGCTGGAGTGCAGTGGCGCGATCTTGGCTCACTGGAACCAGCGCCTCCTGGGTTCAAGCAATTCTCCTGCCTTAGCCTGCCGAGTAGCTGGGACTACAAGTGCGTGCCACCAGGCCCAGCTAATTTTTGTAATTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATGACAGGCATGAGCCACCAGCACCGGTGAGTGTTGACATTTGACAAGTGCCGAGTGCCTGTGGAACATTAATGAAAGACAGAGACTGGAGGGTTCCTCAACTTTGTGGACATTCAACATCTTGATGTTTACAAACACAGTATCCTGAGAATGCATATGTTTTATTGCTTTTATTAAAAAAATTAATTCATTAGCCAAAGTTTCCATAAATCTCACTCAGAAGTAAATATCCTTAGCCAGCCACCTCTTTCTGTCTTTCCTAG
Seq C2 exon
GGACGGTCCCGATCAGAACTCACCCCAGCTGGGAGTTTTCAGTGGCAACACAGCCCTCGAAACGGCGTATAGCTCCACCAACCAAGTCCTGCTCAAGTTCCACAGCGACTTTTCAAATGGAGGCTTCTTTGTCCTCAATTTCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183117-CSMD1:NM_033225:43
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(53.3=93.3)
A:
NA
C2:
PF0043115=CUB=PD(44.8=95.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTGTGGGTACAACGTAACT
R:
CGTGGAAATTGAGGACAAAGAAGC
Band lengths:
322-1731
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)