HsaINT0042175 @ hg38
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr1:33625051-33626581:-
Coord C1 exon
chr1:33626486-33626581
Coord A exon
chr1:33625255-33626485
Coord C2 exon
chr1:33625051-33625254
Length
1231 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
AGTGCCCTTGTCCCCCACAGCGG
3' ss Score
9.04
Exon sequences
Seq C1 exon
GAGAATCACTGCCCTTGGCCACCTCCAATCAAGTTCTCATTAAGTTCAGCGCCAAAGGCCTCGCACCAGCCAGAGGCTTCCACTTTGTCTACCAAG
Seq A exon
GTATGGAGGACATGGACGCCGGAGGTAGGAAGGTGATCTCGGTTCTTAAGGGACTCGTGATCGAAGGGACAGGGATCTTTGACCTCTAGTCTGAGTCCCTTTCTCAGGGTGTTTGGGGGCAGTTACTAGTTTGTAGGGCAATTCCCTGAAATCCAGTTAATTTTATGCATTCACTTACTCAGCAGACATTTCTTAGACAAGTTCTGTGTTTAATGAGGAAGGAAATCAGACAAAGGCAGCCAGTTTTTTCCCCTTCCCCACTCCACCCATTGTCTGGCATGGTCCAGATGGCACTGAAGAGACCAGCCCAGGCATCTTACCTGGACTCCCCTGGAGCTTGGTTTTGTCTGCCAGGCACAGTAAAGGTGCGGGGAAAACACAGGCTTTGAAGTGCCGTGGACATCGATTTGAATCCCACCTCCCCACCTTCGAGCTAGGCTCCAGCTACGCCAGGCCTCAGAGCCTGTTTGCTCACCTGTAAGGAGCGGGCAATCACAATGCCTCACTGATAGGATGCAAAGAGGCTTCGGGAAGTAGCTGGTACCAACCAGCCAGTTGGTGTTAGTTCCCTTCCTTATTGGCCCAGAAAGGTAGTTTGGAGCATCCTGGTTTTCACCCCCAGGTCCCAACCTCTGCTTGCCCAGGAGAACATCCACTTTTGTAGGGCCCAGGTTCTAAGCATGGTCCTGTTCATTCGACTCTGCCCAGGATGAGCTGTGTTTCTCTTTGCAGGAGTGATCCTATCACAGGGGAGGCCATCCCGGGCCCATCAGCCATTCTGGGCGGCAGGAGGGAGGGGAGACTGGGGGTCATGGAGGGCAGGGCCCCAGGCAGGATCTTAAGGCACATGGGGAAAACAGGACAGAGGCAGGGCAAAGGCCCTGAAGGTAGAGGAGGAAGGCCCATTCTCCTTGCTAGGGAACGTGGGACCCTGATGAGTGAGGGGCGTCGTTGGGAAAGCAAAGAACAAAACTGGGCCTAAGGTCTGTGGGAGGTCCACGGCTCTACCTCCCGTGCTTTCCAGGAGCTGTGCTGTAGCGCTGTGTGTCCAACTATAATTCGGTATAACAGGCATCCTCCTAGTTAGCCCTCGAGCCCTTCCCTACGGGAGAGCATCCAGAGCCTCCCAGGGTTTCATCCAGACGGTCTTTGTTCCAGACCCGTTGTATGTCCGTCCCTGGGCCAGTTTCTGAGGGGTGAGGCCTCCCCTCAGTGCCCTTGTCCCCCACAG
Seq C2 exon
CGGTTCCTCGAACCAGCGCCACGCAGTGCAGCTCTGTGCCGGAACCCCGCTATGGCAAGAGGCTGGGCAGTGACTTCTCGGTGGGGGCCATCGTCCGCTTCGAATGCAACTCCGGCTATGCCCTGCAGGGGTCGCCAGAGATCGAGTGCCTCCCTGTGCCTGGGGCCTTGGCCCAATGGAATGTCTCAGCGCCCACGTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904:ENST00000241312:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(28.3=90.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=88.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTGGCCACCTCCAATCAAG
R:
ACACACGTGGGCGCTGAG
Band lengths:
286-1517
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