RnoINT0027626 @ rn6
Intron Retention
Gene
ENSRNOG00000005840 | Cacfd1
Description
calcium channel flower domain containing 1 [Source:RGD Symbol;Acc:1311501]
Coordinates
chr3:5561760-5562967:+
Coord C1 exon
chr3:5561760-5561832
Coord A exon
chr3:5561833-5562841
Coord C2 exon
chr3:5562842-5562967
Length
1009 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TTCTACCTTCGCCCCTGCAGCAT
3' ss Score
9.45
Exon sequences
Seq C1 exon
CCTGTGCCATCTCTGGACTCTTCAACTGCGTCACGATCCACCCTCTGAACATCGCAGCTGGGGTGTGGATGAT
Seq A exon
GTGAGTAGCTGCGGATGTCCTGCTTCGGTGGGGTTCGAGGCATGTGGTGCAGGTCTCATCCCGCTTCCCGCTCCAAGGTTTCCTGAGAGCTGCTTGAGCCTTTATTGGGGACAAGGACACCAAACACAGTCGCAGCGTCTACTCAGCCAGACACTGTAGACTCCTGGTCTACTACAATGGGCCCTTCTCTGTGAGAGTTCAGGGCCATGGTGTGTAAGGTCAGAATTGAGGGTTTATGACAGAGAGGAGGGTAGGCAGCTGTGAGGCCATTAGCAGGGCTAGAGGTAGGAGGCAGGTACAGGTGGAACTGGTGGCTATAGCATCCCCAGGGAGCCCCTTTTCACCCTCCTCCTGGGCAGCTAGGTCGCAGGGAAAGGGGTGACAGAGTGAGGGCTGTTCAGATGCATGGGGGGCACTGCACAGTAGCATTTGCTAGTGCTCACCTGTGGGAGCAAAGGCCGTTAGCACCAGCAGCTTACGTGCTTCCAGCAACTGGGCGGGGCTAAAGGCTCCCAGCATGAGCATCCCACTACCCTGCCTCTCTGTCTCCCCGACCCACATGCTCCCAGCTCAGGCCATGGGTAGTCCTCAGTGGCTCAGTGGCCCAGCCAGCCCTTGCATTTCTGCTGGGGGCAGCCTGCCCTTGATGTCAGTGTTAGTGACTATGGAGACAGTACTAACAACGGGAGGTGTGGCTAAGTTCTGTGGGCTAACGTGCTGCTGGCTCAAGATTATGGAGGCAATCTTAGTTCTTCATTTCACTTTTGGATCAATAACGAGATCAGGCTCTTCCACCGGGATGCTTGGGTGGTTAGGATGCTGGGGCAGCCGTGGGGCAGGGCGGGTTGGGTTGTGGAACTGCTTGGCGGAAACTGGTACCCTGTAGTATCTGGGTGTTTATGGAGTTCAGGGCCTCTGAGATGGCAGTGTTCCTTGAGCCACTGGCATGAGAGCTATTGCAGCTCCTGGTTGTAAACTATCATTGTCCTTTCTACCTTCGCCCCTGCAG
Seq C2 exon
CATGAACGCCTTTATCCTGTTGCTGTGTGAGGCCCCCTTCTGCTGCCAGTTTGTGGAGTTTGCAAACACAGTAGCTGAGAAGGTTGACCGGCTGCGCTCCTGGCAGAAGGCCGTCTTCTACTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005840:ENSRNOT00000007677:4
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:
PF102334=Cg6151-P=FE(21.8=100)
A:
NA
C2:
PF102334=Cg6151-P=FE(38.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTGCCATCTCTGGACTCT
R:
CCGCAGTAGAAGACGGCCTT
Band lengths:
199-1208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]