HsaINT0042138 @ hg19
Intron Retention
Gene
ENSG00000183117 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:14026]
Coordinates
chr8:2815218-2818736:-
Coord C1 exon
chr8:2818663-2818736
Coord A exon
chr8:2815330-2818662
Coord C2 exon
chr8:2815218-2815329
Length
3333 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTT
5' ss Score
5.77
3' ss Seq
GTATTGGATTTCCTCTCTAGGTT
3' ss Score
9.21
Exon sequences
Seq C1 exon
ATCCTGCTCATAACACCTGCCCAGACCCTGGTACGCCACACTTTGGAATACAGAATAGCTCCAGAGGCTATGAG
Seq A exon
GTAGTTCATTATGAATTTACTATGTTTTCTTTCTGGAAATATAAAATATATTTGTTACTTAAACATATGTGAGTGCTTTTTTATATCATACCTTATTCATGTTATATTTACCTGAATAAAATTCGTTCAAAGGGGATTTCTACATGTGTTTTTAACTGTCAAAATCAATATATGTATATATATATATATATATATATATATCTTGCTTACTAGATAATAATGGAATAATGCATAATTTCATATAGAAATTAACATAGCAACTATTACATTATTTTCTATTTGAAATCATGCATGATTCTATTATTTGTCTGTTAAATTCTCACGGCAGTTCTCAGATTGGGGTAACTTGTCACTGATTAGCTACCCATAAAAGGTTCCACTTAGGGACTGGATATAGTGGGGAAATAATATTAAATTCTAGAGATAAAAATAGGAGAAAATGTATGTAAGCCCCTTAGTCTAAACTTACTTGTGAAATTAGTTCTCCGTATGATCTTTAAATTTCTATGAATTATTAGCGTACTAAATATCATTTTGGAACGTTCATTTGACTTTTAATAAAATGAACACTAACACTTCAGTGAACGTTGGAGAAATACCTAAAAGTGGAAGGTAATGAAGCTTGAAATAAAATGTTTTAACCATCTTAAGTACTCCCATAACTTCACTGTTATCTGGTTGGATGACTTTGAAAACAAAAGTTAATTATATAGGGATCTCATCAATTAAGAATAAAAAACCTTCTTCCTCAGCCACTTTCCCCATCTCTCGTGAGCACGAAAATATTCCCATTGTTCTCGCTCGGACACAGAGTGGCCATTTCCTTGTAGCTCTCTTGCATCCCACAGGGGAAGTCCTTACAGGGAGCTAATAATATACTGACTCTAGCACATTTTCTATTATGTCTCAAATATTGCCTTAAACTTCAAGTAAATACTTTCAGGTATATAAATATTTAATGCCAAATTGTCAAGGAATATTGGAAAATACTATATATGGATGTCGCTCTCACTGATTCACTAAGAAAAATAAAATTTTGATCACCATTGCTTTGAGCAATTCTTAACTTGCCTATGTACAACTTACAGTAATTAAAAGTCAATGATGACTGTATTTAGCAACATAGTTCTATAACCTATCATATGACACTAATAGGGTTGGATAAATCCTTCACCCTCCTTATAACAAATTAGTTACACTAACACGAATAATTGATTTTATCCAACAGCAAGATTTACTAATAATTTAAAGAGCCCAGACACCATGTTTTAAGGAGAAGGTTGAGACCATGAAATGCAGCTCTCCCCAAATGTTTTTATTTCTTCCTTTATTAGGAACATTTTAGTTTTTAAAGTAACCAATGAGATTTTTGTCTGTTTTCTTTAGCACCATATGCTGAAACCTTACTTACACAAAGTGAGCCATTTCAGTGTGAAATGTCCCTGTGTTAGGCTATGTTAATCTTGCAGCTTAAATGACTACCTCCCGTTCTCCAGCCAGCGTGTCCCCGAAACCCGTAGCTCCAGGGTTAGTGTATGATAATCAGTTTGCAGTGGCTCGGTATATTCTGCTAAAAAAAAAATTATTGAGAAGGAGACTGTATTTTCTTTCTGCCAGTAAATGATACAGGTTATCCATGACCTTCCTGAGAATGTCAGCATGTTTACCAGGAGGTCTGGTTGGAATTGCAAACATGCTTGCATGGAGAGTTGATGGACACCGTTCCTGATAGAGAGGAAGTGGGCTGGGAGCAGCAGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCCAGGCAGAAGAATCGCTTGAGGCCAGGAGAACAGCCTGGGCAACATAGCAAGACCCTATTTCTACAAAGAATACAAAAAATCATCTGGGCATGGTAAGGTGCACCTGTTGTCACAGCTGTGCAGAAGGCTGAGATGGGAGCTACTTGAGCCCTGGAGGTCAAGGATGCAATGAGCTATGATTGCACCACTGTGCTGTATACTCTGGGCAATAGAGAGAGGCCCTGACTCTAAAGTTTAAATCGATCAGTCAATCAATCAATCAATCAAGAGTAAATGAGTCAACGCTTTCCCATCATTGAATCTTAAATTAGCTATTGATTTGACATTTAGATAAATTTGTACTTTTCTTTATAAATTCATACTTCCACTTTATCAAGTGCTAGAAGCAGCATTTTTTTTCTCCTGATATCCTTTCACACTATTCAGTGTACCAACTATTTCCTTGCATTTTACTTGTAGTTATTCTTCCCGGAATCCCAACATGGGAGGTATGGGCTTATGCCTGTGAGAAGGCAGACACAGGGAATTAAATAACTGGTTAAAATTCTCAGAGCAAGAAACAAGAGGGGAATTCAAATCTTTGGATGCTAACTTGGTGCACTTATGTGCCTTCATAAGTCAAGCTTTAAGGAAATAATCTGGTCCCAAGCCAAGCTGGGATGAGTGCAAACCCGCCTTCCCTGGGGGCTGCTTTCCTCTCCCTGTATACATGAGTCATGCTGGCCTCATGCTGCAGATACACAGAACCATGGATGATCTTTGGTGCCCCTCAACACACGACCATAGCTCATTCTCTAAAAAAGACATTTACAGATCACAGGAATCTGCCCCTCAAGGCACCTCTGGTTAAATTAGGAACACACATGGGTGAATAAATATACAGGTAATTCCAGGACACTGTGGTGAGTGGAGCAGATACGTTGGGGAAATGCATTCAAGCTGAATGTGATTCATTCTTGGAGGATCAGAGAAGAATCTGCAGCGGATGTGCAGTTTAAGCAAAGTACAGAGAATTAAGTGGGGGTTAGCTTTGTGAAGACCTGGTGAGGAAGACGCCTCAGACATTCAGACAACAGTAAATAGTTTGTACAGTTTGAAGCATCAGAAAGACAGGTAGAGTTTTGGTGGACTCTGTATGAGTAGGAGTTGACCAATCCCCTTGGAATGCTAACAAAAGTAATTTTCTAATAAATACCAGTTGTTTCAAATGTGAGTGGCAGGAAAAAAATGAAAAAGGAAATAATAATTATTACAAACAAAAAAGAAAGAACTCTAAAACAGAAAAGGCATAATTTCTTTACCCAAACAGCCGTCTAAATTTTCAAAATTCGAGAAGATCTTACATTATTCATTGAGCAATCTACATTGTGTGTAACACTGTAGCAGGCAGTTAAAATGTACATGTTGACTTAGACAGTGGCTTGACATTAACCTGAAAAGTTGCTGCTGTACTTTTACTCGGGCGTGTACTTTCAGGTATCACTAGTTGACACTTCGTATATTCCCTTGGCCTCTGAAGCTAGTATTGGATTTCCTCTCTAG
Seq C2 exon
GTTGGAAGCACGGTTTTTTTCAGGTGCAGAAAAGGCTACCATATTCAAGGTTCCACGACTCGCACCTGCCTTGCCAATTTAACATGGAGTGGGATACAGACCGAATGTATAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183117-CSMD1:NM_033225:62
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(32.7=69.2)
A:
NA
C2:
PF0008415=Sushi=PD(65.5=94.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
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]
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)