HsaINT0042214 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:33979609-33985277:-
Coord C1 exon
chr1:33985065-33985277
Coord A exon
chr1:33982171-33985064
Coord C2 exon
chr1:33979609-33982170
Length
2894 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
TGTGATCTGTTTGTTCCCAGTTC
3' ss Score
9.25
Exon sequences
Seq C1 exon
GAGAAGACCCAAAGTTCCTTTCAATGGCTATGCTGGCCACGAGAACACCAATGTTCGGGCCACATTTGAGAACCCAATGTACGACCGCAACATCCAGCCCACAGACATCATGGCCAGCGAGGCGGAGTTCACAGTCAGCACAGTGTGCACAGCAGTATAGCCACCCGGCCTGGCCGCCACCACCGCCACCGAGAGCCCCGCCTCCAGCAGCCG
Seq A exon
GTGAGCAGGGGTGTGGGAGGAAGACAGGCCATGACAAGCACAGACAGGGACCTATGCGTGCCAGGGGCTCCACCCAACGGAGTCGCACACACCACATAGACACACCCAGTAAGAGGAGAGCTGTGCATTGAGCATCATTGTGTAACAGGCACTGAACCAGGCCCTTTGTGGATCTAATATATTGAATCCCTGCACGCCCTGTGAGGTAGAAGCTTGTGGGAGCCCCATTACAGATGAGAAAACTGAGCTGCATAGAAACTAACTTGAGCAAGGTCACACAGCTCAGAAGGGGTGGGGTCGAAATCCAATCCCAGGCTGACTGGCTCCAGAAACTGCTCCTCACCCCTGGGCTTGGCAGAACATCGGCATGTACTAGTCTGTTTCTCTCTAGAGAAACAGAACCAACTGGATATATACATCCTCTGGGTCGAAGTCAAGCCCTGGAGATCTGTAGAGCTATACAGAGATGCACATATATCTGTGTATATAGGTATATTGTGTATATATATACATTCATACACTATAAACGCAATACATATACCCCATATCAAGATATATCCATACCTATCCATCTATATATAGATACGCATCTCCGTAGAGCTATATGTAAATGTTATATAGAGATAGAAATATAAATAAATATATATTTAGAGAGAGAGATTCATCTAAGGAATTGGCTGGCAAGGTGGAAATCTAAAGGGCAGGCCAGCAGGCTAGAAATTCCAGCAGGAGTTGATGCTGTCATCTTGAGTCCAAAAGCAGTCAGAGACGGAATTCCTTCCTCTTTGGAGCACCTCAGTCTTTTTCTTAAGGCCTTCAGCTGATTGAACGAGGCCCACACACATTATGGAGACTCAAAGTCTACTGATTTCAAAGTTAATTTTATCTAAAAAGATACCTTCACAGCAATATCCAGATTGGTGTTTGACCCATCAACTGAGCACCATAGCCTAGGCAGGTTTACTTACAAAATTCCCCACATTGAGCACAACAGAGGGGAGGAGCTCCCGGAAATATAGACAGGGGGCAGACACACCCACACGTGTACACGGTCATGCACACACACACACACACATACGCATACATGCACACAGGCATGCATCTGACAGGCCCACTGGGAAGGAACTGATGAATCTAAAAGGCACTGCCTCTTCCTCACTGTGTCCTCCTTCGATGACACCCTCACCTCTGGGACCTATGACCCTTCAGGAGTTGCCCCAACACGATGTCCAAGCTGCACCCCTCTGAGAACTGTCTTCTCCCACACATCCCGCTTTCTGGGGATAGGCAGGTGCCCCCTCTCAGGTCCTGTGCTGAAGGACTCTGGGGAGAAGAGTCACAGAGCCAGCCAGGTAGGGATTCCCAGTGAGGGCGGTGGAAAATCCGCCAAGTGGGCCACCAGCCAAACCCAGGGCTAGTGTTGCGCTCCCTCCCCACGCTCCTGTGCATGGCCGCTCACGTGGCAGATTCTCCCAGCCACACACAAATGGCAGTGCAGCGAGGAAACAGGCTTTTATGAGGGTGCCTGCAAAGGCCACCAACAGAGATGGTGGGGACAGTTCCTGCGGAGGGGGTTACAAGAGCAGCAAATGTCATTATCACTGCCCAGCCCCTGACGTGCTTTACTCCCTTTCTGCCTCACAACTCCTGGAGGATTTCACAGTTTCAGCCTGAGTCCCAGATGGTGAGTGAGTCAGGGACTCAGCAGATGCAGCTCCTGAATACAAACAATTTATGGAAAGAGCTTTTCCCCATCTTTTTACGTCTCTCCAAAACAAACATTTAAATAAGGGTTCCCCCTTATTCCAGTGGGATTGTTTTAGCATGCCAAAATTACTCCTCAAGTTTCATCTGTATGCCCAATCTTTATTTTTTCCTTCTCAGAACTCTTATCAATAGAAGGCAAAAGAGAAAAAGAAAAATCCCCTCTGATGATGTAAATCGGGGCTTGGAGATGATCAGTGATGAATCTGATTCACTGCATGAATTATTGAACAGTGTAAGAAAGAAACAAGAATGCCGCTGACCTCCACACAGTCACTCTTGCTCCACACCTGGGTTCTGCTGGGTTCCAGGTGCTGGTGTGCGCCATGCTGTCACCTCCGGGTCGGCTGGGGTTGGTGGCTCCACATCTGGCCAGCCCTCAGCATTGGCCCCTTGCCAGCAGGCTCTGAACCCACTGCCCAGCCCACAGGTCTCCAGCAGGGCCCCTCTGACCACTTCTGCCCACAGCTGGAGCATAAAGAAAGCAAGAGCCACCCTGAACAGACACACACACATTGCAAATGAGTGACTAGATGGTAATTTTTTTTTAAATAATGCCAAGGAGAAAAGCTGAAATTAAAATAAACACCCTACTAAGGAAGCAACGAGGCCTGTGCGGTCAGTGAGTAACAGGGCGGGGGAACAGGGCTGTGTGATGATGTTTGCCAACCCTTCCTCCATTAAAAAAAAGTATCAAAAATGAGATTTCACAACTGTGTCACTACAAAAATGAATATAATCCAGCCTGGATTCTTTATTACAGAGCCATTATTATCCTAGTCATTTTTTTTTTTTCATCTGATTTTGAAAGAAACTAAAATTAGAATGTTTTCCTGGGTTCCTAAAAGTATGGTGGCCCCCAAGCACTGGGCCTCCAGGTCTAATGGCGAAGTTGGCCCTGCAAGGGAAAAAGACAGAAAAATACATGTTCTGCTGCACGTATTCCCTACCTACCCCCATCCCCAACCTGGGAAGATTAAAAATCAAAGTGAAGATTGAGGTGACTCATCTCTTTCCCGCTTGTGCCTTCTTTTCTTTGCCGCTTTGCTTTTCCTCCTCTGCTCCCGGCCCCTCCCCTCCCACTGCCTCTTTTTTCTTTGCAAACTCAGGTGTGATCTGTTTGTTCCCAG
Seq C2 exon
TTCCCCAGGGGGCAGGAAGTAGGCTCCCCTGAGCACAGTGCCCAGTGCCCATCTTCGTTCGTCTCCTTGCCTGTGTCTGCTACTGCTGGGACTCAGGCCCTCGCCCTGCCGCCATCTATGCCAGTTACCCTGGAGAGGACTCCTGCCGTGTCCTGAAAAGGCAGAAAAGGAAGAGGGGCTGCAGACAGAGGAAGAAAGTTTATGGATTTAAAATAGCAAAGCAACTTGTGGATCTGTGTGTGTGTGTGTGTGTATGGGCCTGATCACACACAAACACACACACCTCTCCTTCATTCACGTCCTATGGAAGAGACCATAAAGGCTTCAAAACTAGAAGTGCGCATGAAGGATGCTTCATGCCCTGTTCCCCACACAGAGAAGAGATGAAGAGGGGGAGGTACGGTCAGCTTTCAAAACAATATGCCCCCCGCCCATCCCATGTGTGAGGACATGGTGACTCGGTGACTGTAACAGTAGGACACATCCCATCATGCGGTCAGAGTGCAGAAACCCGGTCAGCGTGCAGAAACCAGCTGTCTGCTGATGAACGGCCCATCTGCACAGCGGCAGCAAGGATTACCCCAAGGGCAGGAAAAAAGTCTTTGGAAATAGATTGAAAATCAGTTTCTTTATTTTTTTCAAACACTGTTTTATTGAGTTCTAAACCCAGTGGATTAAAAAGTCATTTGGGTCCTGGGAAGCACTGGGAAAGAAGGGAGAGCCGGGGAGGATAGGGCAGGAGTCTGGCCAGGAGCCCAAGGTCAAGTCTGGCTGTCAACTGACAAAGAGAAGAGAAGACAAGTCTGTGGCCCAGACAGGATGCCAAGTCTGGGGGCAGCAGCAGGGTCCTTGAGAGAACAGGGGAGCAAGCCTGCCCCAGTACCCAAAAAACAATGGCTATCATGTACTGGGGTTATTCTCTGTGCCTGACACTTTACCTGTAGTATTTCTAGTCTGCACAATAACACCAAAATGTAGGATTTGTTATTCCCCTTTGACAGATGAGAAAACAGAAGCCTGCAAAGGTAAAGACAGAGTTAGGAAGTGTGGAGTCAGAATGCAAACCCAGATCAGTCTGCCCCAAAGTCCACTACACCAGCTGCCAGAAACCCTGTTCTAGAAGGGGCAGCTAAGAAGGGAGGAGCCGATGAATCTCTACAGTAGCACTGTGGCCAGGTCTGGAAAGCCAGGCAAGACACCTGTGTGTCCTATCTGGGTTCTGCTGTCTCCGCGTAGGCAGCTTCGGGGCAAGGATTCAACTCCCCAGGCCTCCCACGGTTGGTGCTGGCTCCTTGGCTCCCAGCAGCCGCTGACCATAGCCAGCAAAAGACCTGGCAGGTCCTGAATCAAAACAACAGAGTGGCTGAAAGTCACACCTCTCCAGCTCCTTGCGAGTGGGTTTGATTGATTTTGACAGCTATATCATGCTTGGGTCGTTCATGAATTCCATGAGAATTGTTGGGAAGTTCATGAGTTTAGGAATCAAAGTATAGCATTTAGGGCCACTTTCTCTGTCCTCGGGAAGGCCCCCACAAGCTTAAGCCCCTGTATACGTGTGACATGCTGGCCTCAGAGATTCATGTCACATATTGAAATAGCAAATAGAAATGTGCAGGAGCGGAGGGACAGCGACACCTGGTTCTTAAGCAAATTCTAGATTGGAACAATTAGAAGATCTGACTGATGTTAAGAGTGGCCAGAGGAAAGTGAGAGGCGTCCATTTCCAGCAGACACAATGGAGGCTGACAGAGGCAGGAGCCTACCCCTGGCCACACCACCTCTGGGACACGGCACCCCCCTGGGCCTGGAGGGAGAGGGCCAATCCAGACACACTCACACTCTCATCTCTTTCCTTGGCTGGAAACAAGTGCAGGAAGCTCCCCTCCCAATTTCTTATGCTCCCTTCCCCCTTACACTCCTCTCCTTCGACTGCTCCCTTCCCCCTTCTTATGCCCCTCTCAGACCACCCAGCGGATGCCTATTCCCGCCCCCCACCCCTCCCCTGCGTCTCCTTGTAAAGTTCCATGAGATGCTCGAGGAGCACCTGCTGGTGGGGCACCCAGCACTCTGCTGGGCATCACCCTCCGCACCCCTGACATTTCTCTCCACCTCCAGAGGCTTGGAAGGGAACAGGGCAGATGAGGCCCTTCACCCACCATCTACGCCATATACCCATCACCATCCCATGAGGAAAAAAAAAAAAGTAAAACAAAGACAAAAAAAATCTTTTGTACAGAGATATATTTTTATTATACAAAGTTTGTACAGTACCAAAAAAGAAAAAAAAAAAGGTGTAAATTTTTTTTTCATTATTGTAGGTAAACGGTAGTGGAAGCCTTTTTTGTAAATGTAATAAAATGTATAAATATGGTTTTCAGAAAACATCAAGTGCTGTAAATATGTAATCTACACACCTTCTTGGCTTGTCTGCAGTATATACATTTAATTTATCTGTCTCTGTATATGAGGCTTCCCCCTGGGGTCCTGCATTATGGTACTTTCCTGAATTTGAAAGCAATTTTAAATTTTTTGAATTCAAATAAAATATAAATTTTTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:69
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.075 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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
- Genotype-Tissue Expression Project (GTEx)
- 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)