HsaINT0042183 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34076641-34080220:-
Coord C1 exon
chr1:34080104-34080220
Coord A exon
chr1:34076851-34080103
Coord C2 exon
chr1:34076641-34076850
Length
3253 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TGCCTCTGTCTTGCTCCCAGGAG
3' ss Score
9.51
Exon sequences
Seq C1 exon
CACAGTGTGGGGGAACAGTGGAGGAGATGGAGGGGGTGATCCTGAGCCCCGGCTTCCCAGGCAACTACCCCAGTAACATGGACTGCTCCTGGAAAATAGCACTGCCCGTGGGCTTTG
Seq A exon
GTAAGTCTCTGCAGCCCCCAGAGGAGACAGGCTTCAAGCCCAGACCCTTGAGCTTAAAACTACTGTCCGCCAAAATCTCTTAGCACAAACTTGGGCCAAGTCTGTTTAGTACTCTGCCTCTCTGTTTTCTCATCTGTTGACCTCTTGTACAATTGTGAAGACCAATTAAGAATGGCAGAGATTAACATATAGGGGGGAGAAAAATCTTAGGGGTTGCCATTATTATTATTTGAGCCATAAACTAAAATCCAGGAATGTGGAATGAGAAATTACTCGGATTATACCTAACTAACACTGTATCACTTGATATTAAAAATAAAAAATAAAAATAAATTACTCAGGGACTTAAAAAAAAAGGCGGGGGTGGGGCGGAAATCTGTCGTACAGAGACTGGACCTCAAGTTGTACTTTTAACCCCAGTGTCTAATTTATCATCCTAATTAAATTGAGCCAAATCAATGAGAAATCGAGTTTGCATTCTTCTTCGTATGCACATTCTAGCTGGCCTAGAGACTGGGAAGGTTGTTTTTTTGGTTTTGGGGGGTTATTTTTGTTTTGTTTTGTTTTTGGAGCTGGAGTATGCTAGGCATGGGAGGTTGTCAGGGTGTGGAGGACATCAGTGTGGGTACAAAATGTAATTGCTGGTGATCCACATATTATGCACTGGGAATATCATTTAACCCAAATGTCTCTGTTGAAGGGATGAGGGCTTTGTGCTGACATGGAACTGATGGGCCGTACGCACGGGTCATCTTGCCCAAGCCATTGCACTGCTTCTAGGAATGAAATGTCCCAAGGGGATTATGCCTGCATAGCCCTGAATGCCAGTCTGTGAGCCTCAGAAATGAAGATCTCCCATTTTATCCTTCATTATTCAGCCTGGAGTGTGATTAGAGATTAGGGAAGGGGCTTTTGGGAGAAAGCAGTCTAACTGGCCTTCTCTAAATCCGGTTGGAGGGGAGGAGAGAGCTTGGTGGCCCTCTGAAAGATGTTATTTTCTGTTCAGTACCATCTTCTGAAGGAAACTGGGTGTTCAGTACCATCTTCTGAAGGAAACTGGGAGCAAAGCGATGACGCCCTCGGCAGTCTTAGGAGACTCCAGACTTTGAGACATTAAGAGGATCTGGGAGACCCTGTACCTCTGCATCCAGTCTTGAGGCAGAACCAAGATGATAGAAGGTGGGGAGGGCAACATCCAAAGGCAAACAGAAGTTTGAATGAGGTGGCTTTCCCTGTAAGTCCTTATGTTCAGCCACCATTTTCACCTCTAAATTCTGGGTGCTAATTCAGGTTTCAGGGAAGAAGCTACTGCTGGGTCCAGTTGCAAAGGCCCGGGATCCCTTGCTTTCAAGTTAATGTTGGATTCTGCCGAGGTCCCTAACTTGGTACCTGGTCTCAGCGTGTAAAGAGCTGCTGCAGCTACATGCTGCTCCACTAGATGGCGGTCACAGTCCAGTTCTTTCCTTGGAGTTCAAGTCAGAAATTCCGCCATCCTTAAAGAGCCCCTTCTGTGGGCCTGCAGCCCGCAGGGCTCCTATATGAGGGGACGATGCCTGGGCAGTGGAATGGAAAGCACAGGCTCCTCAGATAATGTATACAAAGATGTCATCACAGCCTAACACGGTGAAAACCCGTCTCTACTAAAATACAAAAAATTAGCTGGGCCTGGTGGCGGGTGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATCGTGCCACTGCACTCCAGCCCGGGCGACCGAACAAGACTCTGTCTCAAAAAAAAAAAAAAAAACCATCACAAAATTATCTGCAACTTGGAAACAATCTGCATGTTCATGAGTTGGGGAGTGAACTGTATGGTTGGATAATTCATAAAATGGAATTAACATGCAGTTAAAATGAATGAACTATATTTTTGTATATTAACATGGATAGACCTTGAAAAACACAATATTATGTAAAAAACTGTATGTACAGTATAATATCATTTATGTAAATCTTGAAAACACATAAACCCAGATACATATTTAAGAATCCAAAACCATGAACTGGAAGGATAGCTTCCAAATTCATGTGATTGCTTCTGTGGAGGGCAGGAAAGGAATGGAACAGGGCAGGAGATGAAAGATCTTCAACATTAAGTGTCGAGTCTTTATTTTATTCTTTAAATGATCAGATGCAAAAAGAATTATACTCGTGCTTATTCTGAGCTTATTTGATAGCACAGATAAGCCAATTTTAAAAATGAAAATCCATCTATAATCTCATCGTGCAGCGATAATCACTAATGGCTTAGTCTCCCAGCGTTACCATGTAAGTCTCATGAAGACAAGGACCTTCTTGATCTTGCTCATCCTGTACAATGCCTAGCACAGCCCTGATGTACAGCAAATGCCCAGCAAATATTCCTAGCAGGCAAATTAATATTCTTCCATGTTTTATAATACAAAAATTAGAATTGTATACAGCATACTATTTGTCATCTGATTTTTACAATTATCAATGCAATATGGGCTTTTTCCTATGCTCAGTAAATATATTTCTTCAATAACATTTTCCATGGTGATCTAATTTTGAAAAATCTTATCAGTAAACAAACATAAATGTTCCCACCTTCGTTCTTGAAAGAGTATATTACTATGTACATTAAGAACTTAATTAGATTTATTTAACCTGTCAGGTTGCTAGAATGTCTTGATTAACTCACTAAGATCCCAAAGTAGAAACTTTATTTGGCTTCTTTATGGAACAGAGGGGACAATGTATACTTCTAAGCCCTACGTTTCTGAATTATCATAAGAGTTCTAGAAAACAGCAGTATTGAAGGTCTTGTCTTTTGATTAAGTATTGGGGGTGTTATTTTTAAATGAAAAGTTTATTCTAGCAAAACTATCTTTATGCTGATATTGGACATATGAATCATAAATTTAAACAAGTGTTGACCCTGAACTTTGTTTTCAACAAAATAAAATGAACTCCAGTGGAGCTCTGAAATGACTGATGCCTTTATTTTTGAATGAATAATACACTTTTAAGTTCAGCCCTGTCAAAGACAAGAGACTTGGCTGGACGGGCAATTCCCAAAGCCAGTTCTAGGAGCCTTGGCTGGGTGGGAAATCAGTAGCAGGGACTCATGGCTCTGGCAGGAGCTGCTTTCATGAGGCAGCACACTTGAGGCAGGACTGTGTTGCTTTGGGCACTGTCTGCCTCTGTCTTGCTCCCAG
Seq C2 exon
GAGCTCACATCCAGTTCCTGAACTTCTCCACCGAGCCCAACCACGACTACATAGAAATCCGGAATGGCCCCTATGAGACCAGCCGCATGATGGGAAGATTCAGTGGAAGCGAGCTTCCAAGCTCCCTCCTCTCCACGTCCCACGAGACCACCGTGTATTTCCACAGCGACCACTCCCAGAATCGGCCAGGATTCAAGCTGGAGTATCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:40
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=0.104
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(34.9=92.5)
A:
NA
C2:
PF0043115=CUB=PD(64.2=95.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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)