DreINT0047525 @ danRer10
Intron Retention
Gene
ENSDARG00000103340 | clic1
Description
chloride intracellular channel 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3202]
Coordinates
chr19:17470263-17471994:+
Coord C1 exon
chr19:17470263-17470660
Coord A exon
chr19:17470661-17471884
Coord C2 exon
chr19:17471885-17471994
Length
1224 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
ATTTGTGTATTTGTTTATAGGCA
3' ss Score
8.52
Exon sequences
Seq C1 exon
TCGTCGAAATCAGGAAATGAGAGAGAGCGAGAGAGAGGAAGTAGGTTAATCTTGCTCTAGGCGTTATCGATGAATTTCGATACTGAATAAGTAATTTAAATTATTTATACAACATACATTACACTAGAATTGGACACTTTCTGGCGTTCATAGATACTTTGCTCTACATTTAACAACCACTGTCAGATTCGGAGTTCAAGGGAGTGAAGTTTCAAATTGACCACGACATAGAGGAAGTGAGCTCGGTGATAAAGCGGCAGGAGTACAATATATAAGTTTGAGTTAGAATCTCAGTATCGTAAAGCGATATAAATATTCGTATTTTGTTTGAAGTTTGGTTTAACAGTTTGAACTCCAGCATGAGTGAGGAGAGACCTGAGGTTGAGCTCTTCGTGAAG
Seq A exon
GTGAGTTTACCCGCAAGCCATTATTGATACATTTATAAGGACTAGAGTTTCAACTGACAGGCAGACAACGCATGGATCTTTACATTATGAAATAACAAAAAATAAATAAATAAATAAAAATCCAAAAGGAATAGATATTATTCTTATTTCTATTTTAGAAAACAAGTAGTATTCTGCATCACAATAAAATTTGCAGTGTTATTATTATTATCTATTGTTCTTAGTGTTGCTGTGATTCTAGGTTGTAATTAGCATTACTGTGCGTTATATGCACTACACAGACATGCCACATGCTACCAGTACAGCATCAATACTTCCTGTAATGTACTGGAGTGATATAGCACAATCCTTTTGAATTCTTTTTTCAGTGAGTGTTTTTTTAACCCATCTGTATGTATGTAGTTCAGAGATGCTTAATTTAGTTTTTCCTGTTTCACTGGAAGCAAGTTGAGATTTAAATACTAATATATTATAGCCTAAATATATAATAGTACAACATAGAAAAACTTTACACAGACGTGCATCTGTTGGCGTTTTTTGCTAATTTATCTTGTAGAGCATTTATGAGATCAGACACTGCTGTTGGCTTGGCTCAAAATTTCTGCTCCTGTTCAAAACATATATTATGGGGTTTAAGTCAGGGCTCTGTGTGGGCCAGGTACATTTTTATACACCATTACTAATCCTGTCATTTCTTCGTGAACTTTTATTTGCGCTGAGGCAGTCAGGCTTACCCAAACAAAAACGTGATGCATGCATGCTGTTTTTTGTTTGAGTGCATGAAATAAACTCCCTTGTATTGTCATTTTGCATAGTCACTCTTTTGTTTTGCTGGTATACAAAATTGACTATCAATGTTCTTTAAGAATAAATTACTTCCTGTCACAAAGGACACTTGACCTAATCATCTTGCATTTGGGTACAATATGATTCCTTGTATGTACAGATGTTAAAAAAGTTTCTTTTTGTGATTAAGTGCAAGGATAACAAGGGGCTACACCATGGGTGCTCATCCATACTCCTGGATATACCATCTTGCAGAGTTTAGCTCCAAACATAACTAAACCAACTAAGAAGTATCTAAAGGATCACTTGGTAATTAAAGACAGGTGTTTTTGATCAATGTTACAGATAAACTCTGCAGGAAGGTTGATCTTCAGGAATAGAGCTGAACCCCCCTGGTCTATACACAGTCATTCTCTGAATTTGTGTATTTGTTTATAG
Seq C2 exon
GCAGGAAGTGATGGTCAGAGTATTGGAAACTGCCCGTTTTCTCAGCGGCTTTTCATGGTCTTGTGGCTAAAAGGCGTAACTTTTAATGTGACCACAGTTGACATGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103340:ENSDART00000158935:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134171=GST_N_3=PU(41.7=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGACACTTTCTGGCGTTCA
R:
CGCCTTTTAGCCACAAGACCA
Band lengths:
345-1569
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]