RnoINT0027628 @ rn6
Intron Retention
Gene
ENSRNOG00000005840 | Cacfd1
Description
calcium channel flower domain containing 1 [Source:RGD Symbol;Acc:1311501]
Coordinates
chr3:5565694-5566613:+
Coord C1 exon
chr3:5565694-5565801
Coord A exon
chr3:5565802-5566212
Coord C2 exon
chr3:5566213-5566613
Length
411 bp
Sequences
Splice sites
5' ss Seq
AAAGTGCGT
5' ss Score
5.93
3' ss Seq
ACCTGCTTCTCTCTCTGCAGGGG
3' ss Score
12.56
Exon sequences
Seq C1 exon
GATGGCCATCGTCCCCATCGTCATGAGCCTGACCCTGACTACACTGCTGGGCAACGCCATCGCCTTCGCCACGGGGGTGCTGTACGGACTGTCTGCCCTGGGCAAAAA
Seq A exon
GTGCGTCTACAGCCCAGTCCCGGGGTGGGGCCTCCTCTGCTGCCCCTGCTCTCCCACCTGAAGAGGGAAAGGTCTGAGTGGGACCCTTTGTCTAGTTGTTATGCAGTGGCCACAAGTGAGTTCTCTGTGCTCAGGAACAGAGGCAAGAAATGAGGGACAGCCTCAGTGGTCCCTCTTGACTGGCTTGCACATAGGTATGCAGCAGACATTGCAGCCGACTGCCACCTCTTCCCTTCGGCTCCGTCAGTGCCAGGCAACACGCGCCCCTCAGAGTAGCAAACCTCTGCCTCCCCTTTGACAGTGGCCCCTGGGGAGCACAGTCCTGGGGGAATCTGGTTATGTCTGGGATGCAGCCTGGGGGTTGGAGGTGGGAGGGCGAGGCCTACAGAACACCTGCTTCTCTCTCTGCAG
Seq C2 exon
GGGAGATGCCATTTCTTATGCTCGGATCCAGCAGCAGAGGCAGCAGGCGGATGAGGAGAAGCTGGCTGAGACATTCGAGGGGGAACTGTGAGGTGAGGCAGGGCGCCTGTCCTCATTGCCTACTGCCACTGGGCTCTGTGAACTTGTAGAAGGCTGAGTGTCAGCTCTGCTGAACATCCTGGGACAGGAGTACCTGCAAGTCTCCATGCCTCCAGTCTGCCTGTGCCTACCCTGTTCTGCGGACCTCCTGAGCCTGGAGCTCCTGCCCCACTAGTACTGAAGGCCTGGGCTGCGGGATATGGATGGGGTGAACTCACTCCTGTCAGCCTGTGGCACAGATGCTGTGCTGGTGACCCTTCCCAGGCCTAAGAGCAGTGTCCCCTGAACACATCAGTCCTCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005840:ENSRNOT00000007677:6
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:
PF102334=Cg6151-P=FE(32.7=100)
A:
NA
C2:
PF102334=Cg6151-P=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACTACACTGCTGGGCAAC
R:
GCCTTCAGTACTAGTGGGGCA
Band lengths:
358-769
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]