DreINT0046628 @ danRer10
Intron Retention
Gene
ENSDARG00000101735 | chn1
Description
chimerin 1 [Source:ZFIN;Acc:ZDB-GENE-040426-1934]
Coordinates
chr9:2559509-2560501:+
Coord C1 exon
chr9:2559509-2559646
Coord A exon
chr9:2559647-2560395
Coord C2 exon
chr9:2560396-2560501
Length
749 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TGTGTGTGTGTGTGTTTCAGAGC
3' ss Score
12
Exon sequences
Seq C1 exon
ATGGAGAGAAGGCCGACATCTCAGTGAACGTGTATGAAGACATTAACGTGATCAGCGGAGCTCTGAAACTGTACTTTAGGGACCTGCCGATCCCCGTCATCACCTACGACGCTTATCCTCGCTTCATCCAGGCTGCCA
Seq A exon
GTGAGTCTCCTTCACTATATATTTATTATTATTTAATAGTTATATATTATTATTATTTTTGTTCCAAATTTATTTTGACCTTTTGCCACTTTCATTAATTGTTTTTTATTTATAATGTATTATTTTGTTTATTTACAATTTTTTAAATATATACTGTTGAAGTGAGAAATATTTGCCCTCCTGTGATTTTTTTTATTTATTTTTTATTTATTTATTATTTTTTTTAATATATCCCAAGTTATGTTTAACAACACAAGGAATTTCTCACAGTATTTCCTATAATATTTTTTCTTCTGGAAAAAGTCTTATTTGTTTAATTTCGGCTCAAATAAAAGCAATTTTTAATTTTTTTAAACCCAGTTTAAGGTCAATATTATTAGCCCCCTTAAGCAATATTAGTTTTGGATTGTCTCCAGAACAAACCACTGTTATACAATGACTTGCTTAATTACCTTAACTTTACCCTAATTACCCTAGTTAAGCCTTTCAATGTCACTTTAAGCTGTATAGAAGTATCTTGAAGAATATCTAGTCAAATAAAATGTTCTGTCATCATGGCAAAGATAAAATAAATCGTTTATTAGAGATGAGTTATTAAAACTGTTATGATTGGAAATGTGTAGGAAAAAATCTCTCTGTTAAACAGAAAACGGGAAATAAATATACAGGAGGGCTAATAATTCTGACTTCAACTGTACATCGGGCATTAATCTCTTAAATTTTGATGTGTGTGTGTGTGTGTGTTTCAG
Seq C2 exon
AGCTGACAGATCCAGATGAGCGTCTGGAGGCTCTTCATGAAGCTCTGAAGCTGCTTCCTCCTGCTCACTGTGAAACACTGCGATACCTCATGGCACACCTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101735:ENSDART00000172624:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(29.7=100)
A:
NA
C2:
PF0062022=RhoGAP=FE(22.6=100)
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:
TGGAGAGAAGGCCGACATCTC
R:
CAGGTGTGCCATGAGGTATCG
Band lengths:
238-987
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]