RnoINT0037270 @ rn6
Intron Retention
Gene
ENSRNOG00000029682 | Clic1
Description
chloride intracellular channel 1 [Source:RGD Symbol;Acc:1303043]
Coordinates
chr20:5040337-5042489:+
Coord C1 exon
chr20:5040337-5040589
Coord A exon
chr20:5040590-5042379
Coord C2 exon
chr20:5042380-5042489
Length
1790 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GGGGTGCCGTTGCTTTTCAGGCT
3' ss Score
7.34
Exon sequences
Seq C1 exon
AGGGAACGAGGTGGAGCAGCTGGGTGTGGGGTGCACTGAGCCGGTGGGTAAGCCGCGTTGGAGAGAACTAAAGGGTCTGATCGGACTTAGGTTGCGCCGAAGGGACAGCTCTGAGTCTGGAGGAGAGAATCCCGGGCCGTGAGACCCGCCTTCCCTTGCCCGGGCCCCTCCCAGTTCCCCCAGCGACGGCTGCTTCCTGGTCCCCGACGCAACCATGGCTGAAGAACAACCTCAGGTCGAATTGTTCGTGAAG
Seq A exon
GTAAGAACACCTTCTCTTTCTTTGGCCACTCTCAGAATTTCTGCAAGCCAATCCTCCCCTCTCCTGGGCTCCAGCTCTAACTCCCCAACCCCTTCCTAGTTGACCCCACCCCTAGCCCTGGCGCTGTTTTGCTGGGAGGTGGGGGTGACTTGTGAGACGGTAATGAGAGTTCCAGACTCTCTGAAAAGTTTATGGAAGAGGTTTCCAGCAGCTTAAAGGAGAGAAAGGTGAAGAAATGGGGTTTTCAGAAGTGAGAGAGTGAATGGGGTACGGTGCGGGGTTCGGGGGGGGGTGCAGACGACTGAAGGACCGAGAAAGGGACAGAGGTGGGGTTCAAGAAGAAGAATCGGCTAGGACGTGTGGCCCTATGAAAGAAAGAAAGATGGGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATCTAGAAGGGTTGAAGGATGAGTGTGTCGCAGAGTGGAAGCAAAGAGCCTTCACGAAGCAGCACAATCAATGGCTGAGATGACTATCCCCCCACCCACCCCTCCAGCTAAGGGAGGCTAGAGACTGTGAGGCAGGAAGGAGATTAAAGTTTAGCCATAGTTACTTAGGAAGAGAGGAGAGCTCCAAAGGGGACAGGAGACTCCTTGGGTTAGATTAAAATACCGGGGCTGATGGGTATGGAAGAAAAAGCACCCCCCCACACTGCCCTCCTCCTTCATGCCATCCTCTCCGTGGGTGTGGTCAAGGAGAGATGGTCCTGGGCTTTTGGGTTCAGAAACCGGTGGCTGCAGCTCTCCTCCTCTGCCCAGGCCCGGCCACTCCGGCATCACCCTTCCCCATACCCCCATGCGGTCCCTTCCTCTCCGGGCAGGTCTCCTCCCAGTGGGTGCACATTCGCACCCCCTTTTGCTTCTCCGCCTCCCTTTGCACTCCTGGTTCGTCTTGTCTGTGTGTTGGGTGTCCTGTTTATCTCTATGCTTTTTTTTCCCCTCTGGGTTTTCCCTGGCAGCCTTTCCCAGTTTCTTGGCCCTGGGAAGAGAACTGGAGCCTAGGTCCGCCCCTTAGGTGTGGTCCCCACCTCACACTCGCCTCCAGGGGCTATTTTTACCCTGAGTGAGGTGATGCTGTGGAGATGTTGGCCCTGTGTCCTGTGAGGAGGATCTCAGAGAATCAAAGAACGAGAAGAGTGAGGATTTGGGGAACTGGAAGGGTGTCAGTAGCTGCCTAGGCCTCTGTGAGTACAGATCCCTGCCCCCACTTCCTTGCCGGGAAGGAAGCTGCTGAGGCCTGAAGACACAGAAATGAATCACCCTCAGTCTAGGGGGAGGTGTCCCTTGGGGGATGAGGTCACCTGCATCCAATTAGAGAGTTGCCCCCTTTGTTAGGCCCTCCATATCGCTAAGGTGAGGTTAGGTCCTCTGGCTCACCAGCCCAGCTTCCAGAAACAGCTTGAATAGAGGTTTAGAGAATGGGGACCCGGTTTCCAAACCCTGCCCTACCTCTCTGCTCCACTGGAGAAGATCTAGTATTCAATTCCAGCCCCACCAAGTACCCTATTCTCCACCTTTTGGATCCTGATTCTCAAAGCTAGCCAAGACTTAACTGTTCCTCTGCCTCCTCCCCCCTGTCAATCACTGGGATGCCACCGGCGCCTACCTTTGCTGATCCAGGCCCAAAGGGGAAAATAATTCGGCCCTGGGGGTGGCTTAGACGTCTTAGCAGTGTCTGTCAGGACTAGCAGGAGATTCAGAGAACAGGTCTGGTAAGGATGAGGTGCACCAGGCCTAACTCTGGGGTGCCGTTGCTTTTCAG
Seq C2 exon
GCTGGGAGTGATGGCGCCAAGATTGGGAACTGCCCCTTCTCCCAGAGACTGTTCATGGTGCTGTGGCTCAAGGGAGTCACCTTCAACGTTACCACCGTGGACACCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029682:ENSRNOT00000068435:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134171=GST_N_3=PU(40.8=78.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACGAGGTGGAGCAGCTG
R:
CTTGGTGTCCACGGTGGTAAC
Band lengths:
358-2148
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]