DreINT0046629 @ danRer10
Intron Retention
Gene
ENSDARG00000101735 | chn1
Description
chimerin 1 [Source:ZFIN;Acc:ZDB-GENE-040426-1934]
Coordinates
chr9:2560396-2562211:+
Coord C1 exon
chr9:2560396-2560501
Coord A exon
chr9:2560502-2561161
Coord C2 exon
chr9:2561162-2562211
Length
660 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
GTGTTTACATGTGTGCGCAGGGT
3' ss Score
8.65
Exon sequences
Seq C1 exon
AGCTGACAGATCCAGATGAGCGTCTGGAGGCTCTTCATGAAGCTCTGAAGCTGCTTCCTCCTGCTCACTGTGAAACACTGCGATACCTCATGGCACACCTGAAAAG
Seq A exon
GTCAGAAATCGCAATCGACACCCGTCGTCATTCCCTGTTTCAATCTGCAGTCCTTTTGGTGTTTAACTGTTTCTTTAACAATTAATTTAACAAACATTTCCCAGGTAAAATGTTTGAAATAGTGAAACTGTGGAACTTATGAGTGGTTCAGTACAGGCCACCTTTATCAGTCTTGCGTTTCCACTGCCAAAAGGGTACAAATGTTACCCTTTTATAATAATATAAATGTTAATGAAATATTAAATGAGAAAACAGTGGGCGTGGCTTGTTTTTTTTTTTTTTACTGTGATCTGATTGGATGCCGTAAAGTAGGCATTTTATTAAGAGACAGTTATTACAACCTAACAGACGCCTCCCTTTAACCATTTATGTTTATTGTCATAGCGATGTCGAAACTGACTGCTGGAAGGGCGTGTTTAAATATGTTAGCCACGCCCAATACCTCAGACAGATATAATCTGAGAATTTAACTGAAAACAAACAGGAAGCGCATTTTTAGATTTCAATTTTGGGAAAGGCAAACATTGTTTTTTTTTTTTGGTCTTAATGACAAGCACAGATGAATTGTTCTCCACAAAACTAGCAATGTGAGCTAACAAAATCAATATGGTTAGTTTTGATTTCATGTGTACTTAGCTCGGTGTTTACATGTGTGCGCAG
Seq C2 exon
GGTCACTCAGAATGAGAAGGATAACCTGATGAACGCCGAAAACCTCGGGATCGTCTTCGGGCCGACTTTAATGCGGGCTCCAGACCTGGACGCCATGACGGCTCTAAACGACATCCGCTACCAGCGGCAGGTGGTGGAGCTGCTCATCAAAAATGAAGATATCCTCTTCTAGCACTGTTCCTCAGACTCTGGACTCAAACATGAAGGACTGCTGTATTATAGGACTTCTTTTTTCGGACCGTTGTACTTTTTCCAGCTTCTCTTCTGTATTTTTTGCATGTCTTCCTCCCCATTTTTGTCGGGGGTCGCTGGAGCCGAAGAGGCGGAGTTTAGCGATGTGGGCGGGGCCTATTCAGCGTTATTATGCGATGCCGTTTTTCGTAAAAAAAATTGTGAATTTTGATATCGTCAGTTTTGGAGGTACTTCATCCGATGAGCCGTCAATGTAAAGATGCCGATAATAATGTCGACTTCCGCTATATAACGTCTTACACTGAAACAAAACTTGATTTATTGGGTTTACTCAATTTTTATTTAAGGTAAGTGTTTGCAGATTGCTTACATGGGCTGGATTTTATCAAACAATTACAATTTAGTAATGTTAAACGTAATTAGCTTGTTTAAATTCAACCCATATAAATAGTTTGCAAACATTTACCTTAAAAAAATTGAGTAAATCCAATGAATCTTTTTTTTCCAGTGTATTTAGACAATCCTCTCATGTTTTTCATTTCATTTTGTTTTGTTTTGTTTGTTTTTTGCTATAAATGTCTGTGATTGGGTTATGGCTCTGCAGGTAAAGTGCCAACAGTGAGTTTTTTTAATTATTATTATTATTATTATTTTTAATAATCCGCTTTCTCGAGTCAGATCTCCTCACCAGAGCGATGAACTTCTGCTGTAGACGGATATTCAGGAGGAATATTCACAGTCCATGTACATTTCGACCTTTAGAAACCCCCTCATGACTGCTTGATGTTTTTTTGGTTCTGTGTTTTTGTATTTTGATTTGAGCATGAAGACGTTAATTTATTAAAATGTTCTTTTAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101735:ENSDART00000172624:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(22.6=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(21.3=56.9)
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:
GCTCACTGTGAAACACTGCGA
R:
CCCGACAAAAATGGGGAGGAA
Band lengths:
347-1007
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]