HsaINT0036326 @ hg19
Intron Retention
Gene
ENSG00000169504 | CLIC4
Description
chloride intracellular channel 4 [Source:HGNC Symbol;Acc:13518]
Coordinates
chr1:25166351-25170815:+
Coord C1 exon
chr1:25166351-25166532
Coord A exon
chr1:25166533-25167263
Coord C2 exon
chr1:25167264-25170815
Length
731 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTGATCTCTTTGTATTTCAGGTG
3' ss Score
11.72
Exon sequences
Seq C1 exon
CACTGGAGAGGGGTCTCCTGAAAACCCTGCAGAAACTGGATGAATATCTGAATTCTCCTCTCCCTGATGAAATTGATGAAAATAGTATGGAGGACATAAAGTTTTCTACACGTAAATTTCTGGATGGCAATGAAATGACATTAGCTGATTGCAACCTGCTGCCCAAACTGCATATTGTCAAG
Seq A exon
GTAGGTCTGTAGGGGTTGATGTCGCATTGCCATTACCTTGTATTGTATTTACTAAAGTGGCATTTCCTTTGTGCTCAAAACATTTCTGATTTTATATGACTAGTTGTTTAACTCAATGCTGTTTAGGCAATAGTTGAAGCACCCTAGAGTTAGTTAAATGGAAAATTATGTCTTAAAATTGAGGAATATAAGAAAGATGAATATTTTTTTTTCTGTGACTGCATACAAATTCAAAGATATAATGCGTGACTTTGAATTGGAGTTTGCCACACTGACTTATGTTATCAAATTCTGTTCTGTGATCACACCTTGCTTTCTCTATTGAAGGCAAAAAGTATTGAGCATTTATTATATGAGACACTGGGCTGGGCACATTGTTAAATAGAATAATAATAAGCGCTAGTTGTAAATAAAGACCTAAGATAACAAAAACAGATCTAAAATAGCATATGTGTGTTGTGAAGTATTTTCCAGTGATTATACTTGGCTGTCTTTCTGGATGTCCAAGGCAGTTATTTGCAGTCACTGTCACACTTCTAAATCCCTGGTGTAGCTTGCAGTCTTGGTCATTATTTAAAACTCTGGTTAGAATGATGGTGATGGACTTTTTTTCATATAGAAGCAGTTCTCAAAGATTTAGAGCATTAATTATTTGCTCCAAAATCAGAGATATGTCTAGTTTACAAGACGTGGAAATAAGTCTGTTAACTTTTGATCTCTTTGTATTTCAG
Seq C2 exon
GTGGTGGCCAAAAAATATCGCAACTTTGATATTCCAAAAGAAATGACTGGCATCTGGAGATACCTAACTAATGCATACAGTAGGGACGAGTTCACCAATACCTGTCCCAGTGATAAGGAGGTTGAAATAGCATATAGTGATGTAGCCAAAAGACTCACCAAGTAAAATCGCGTTTGTAAAAGAGATGTCTTCATGTCTTCCCCTAAGAATACGCTTTTCCTAACAGGCTACTCCTTCCTGTAGAGCAGAAATTGTATTTTGCACGAACATGCAGTTATTGAAGATTAGGATCAAGGATAGACAAGGTATAGTAGTTATCTTAAAATATACACTCCTAAGCAGTATTATTTTAAAATCCTTTACCCTGGCTACCTCCCCTACCCGGGTTCCCCTCTCTTTAATTTGGAGACACTCCACCACAAACTTTTCACTTTAGAGGTAGCTTGCCATCTCTCAGGAGCCCTCACCATTGTGTCCATTCACTGTGTATAGATGGCAGAACTTTTGAGGTGCAATGTTTAATTGTTAAAAATAGTAGCCACGACTTTATCAGGCAGCCCCAAACTGGTGCATAATGCATGGTACAAGAAATATTTATGTATTTTTTGGAATTTTGTAATATTTAGTAAGAGTATATGAAAGGATTGCTACTGTATCAGAAATATTGTTTCAATTTAGTCTATCCTGGATATGTACTAACGAATATTACCACCAGAGAAGAGAGCTTTCTACAAAAGTCACTACAGATTTTGCTATATTGCTTTGTAGATAGATTTTTACTTTTGCCTAAAAGCATTTATCCTTCATACCAATTGTAACATCTGACACCATGTAGAAGCTAAAAGTTTAGAGGGAGTGAGGGTTTTCTCAAGACCTTCCTCAAGCATTTTATCTTTAGAAGAGAAACTGATGGGCACCTGATACTCTGTCTAAATACGTTTGTTATATGTGTTTTGCCCTGTGCCATTCATTTGGAACTTTATTGCATTCTTTATTTTAAAAAGCTTGTTTTTACGTAATCATAGAGCTTGCTATTTGTACATCTGTTGAGCAACACTACATAACTGATTTTTAGTTGACTTAGCTATAGCAGTACAATGATTAGTAATGTAAAAATTAACACAGAAATTAACCTAAGGAATGAAGGGTGGGTTTGTCAAAATATCAAGTAAATTTTTGTTTCTAAAGTACATTTAATGTAGATGACCTAAAGAATGCGTTATCCATCCTATATAAAAGAAAGATAAAACACAGGTCACCAATTTTCTCATTTCACCCCATTTACCTTGTATAGAGGATTGTTCATTCCTTTGGGACTAAGTTATAGTTATGGTGAGTGTGTATTTACTGTAGTTTTGCCTGATCTCACTCATTGCACTTCCTGGAGTTAAATTTTCCAACAGCCATGTTGAGGAATAGCACTCTGCATGTTTTTGTTTTGTTTTTCGGGGTTTTTTTTAATTGAAGCCCTAAACCAGGAATTATTTGTGTTCTAACAGGAGGATGAACTTGCTGAAAATAAAACTTTGCTATGTATTTACTCTTTTTTAAAAGACAAAAGCAAAACCAGACTTTCTACGTACTACTCCAAAGACTGTGATTGTGACTATAATACATTTTTGGTAATTTTTTTATACCTAATTTGTATAGGAAGTGCTATTTCTCATAGGCTGTTTCTTGAAATTTTAAGTTTATTGCTTTAAAATGGCAGTGTTTCTCCCACTTTGATATGCTAACATTTAGTAAGCACTGGCTTTATGAAAGCGGCTTTTTATAAGTATACTGCATTTTTTGAGCCTATCATTAATTAGCTTAGTATGAAAGATAAGAAAATCTCCATGTTGTATCCATTTGGCTCAGGAAGATTCTTTGCCTTACCTTTCTTAGAACTCTTTATTGCTTATCAAAAGTTTGAGTACCCGCTTGGTTTTTTTTTGGTAATTAAATATTGTATGATTTATCTGGTTCAAGGAAGATGCACTATTCAGTTATCTATTGAGAAATTATTTTGCAGTGGTTTTAGTGGGTGAAAATGTCCCATCTGCACCAGTACACAGGCAGGCATTATCATTCTTCACCTACTTTTTAAATAGTGGCAACTTGGGATTCATTCTGGTGATTCTGAACCTTGCCTCATAGCTTAAAGTATAAAAAAGATTCAAGAGCAGTGAGGTTTGTTCTTTCCAGTGAATGGTGGACTGAGTGGTGCGAGGTGGAGGGCTAACAAGAGGAAAGAACTACATTCTTCAGAATACAGTGATGAAAATTCATTTTGAAACTCAAATATTTTCATTTTGGATATTCTCCTGTTTTTATTAAACCAGTGATTACACCTGGCCATCCCTCTAAATGTTCTAGGAAGGCATGTCTATTGTGATTTTGATGAAGACAGAATTATTTTTCTCTGTAGAAACACAGATACCACTTTATCAGGGAAGTTAGTCAAATGAAATGGAAATTGGTAAATGGACAAAAGCTAGCTAGTAAAAAGGACGACCCAGCAACATGCTTTAACCCCATTGTATGTTTGTGGAAAGAGCATAGTTTAACATCTTGAGAAATTTGGGACATAAAGTTTTCATGGTAGACAGTTCATGCAGTATATGAATTGCCATAATGGAAATAATCTGATTTTATTTTTACAACTAACATCCATTCCCCTTCATTTAAACACCTTTTGTGTTTTACTTCAGTGAGGAGATTGGAGTCTGAATGGATCTGTTTTCCAAGAGATTCTGAGAAATTTTTGTATTCAGCAGTTGGAAAGCTCTCTATTCTAGTTGATAAAACTTCCCTTTTTTGATGTAGATGCAGATATTCTATACAGTTCTGTTGTCTTTTACTAGGACTGTAAACTTTTGTGATAAAATTCAAATAAGATTTTATTTCTTGGTAATTTTGGCTTTCACAATTTATCTTTAAATCCTTGAGCAATCTGTATACAATTAAGAGATTTCTGACATTTATTCTTACACTAAATGGATCAACTCTAGGATTTAGGCATGTTAACTTCTGTTGTGTTTTGAATCTCTCCAGAGTTGCATGTAGATAGCATTTATTTCTGTGCCCTTAAACCCATTTAGAAAATAACTACAAAGTAAAAATGTAGAGGAAATAGAAATGTATTTTTTCATGAACATTTTGATACAAATTTCATCATTTAATGATTCACCAATTTCTTGCATTAATTTGAATTTAAGCATTTAATTCAAAGAGAGGGGAGCATCCATTATTGATACATGTGGGCTTTTAAAAACTCCATCCTTTATAAATAGTCAAGGTTTGGGCCACACAAAGTATATTTTTATCATGGAAAAATTTCAACTCCTCAAGCCGTAATGTTGAACAGAATTGGAGTATTTTCTTTATAATTTCTTGAACAGGCAAATGAAAGCTTATTATAGAATGCATGTATTTTCTTTTATCTTTGGAACATCAGCACCAGTATATTGCTGGCAGCTATTGTATTAAAAAATAAAGTATATTTTCACTATCATAAAGGATTCTTTTTTCCCCCCTCATGAAAATAAACAACAACTTGGGGTAAAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169504-CLIC4:NM_013943:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134101=GST_C_2=FE(65.2=100)
A:
NA
C2:
PF134101=GST_C_2=PD(25.0=41.8)
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:
GGTCTCCTGAAAACCCTGCAG
R:
ACGCGATTTTACTTGGTGAGTCT
Band lengths:
344-1075
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)