RnoINT0028211 @ rn6
Intron Retention
Gene
ENSRNOG00000008031 | Cacna2d4
Description
calcium voltage-gated channel auxiliary subunit alpha2delta 4 [Source:RGD Symbol;Acc:1562038]
Coordinates
chr4:151302962-151304553:+
Coord C1 exon
chr4:151302962-151303021
Coord A exon
chr4:151303022-151304390
Coord C2 exon
chr4:151304391-151304553
Length
1369 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
GTTCCCCCTTTTTGCCCCAGTTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
AGCCTGGTGGAGGCCGCTGAGGAGGCTGACCTGAACCATGAGTTCAATGCGTCTCTGGTG
Seq A exon
GTAAGTCCTCTAGGGAGTGGGTGCTAGGCTGTGGCTCTGCCCCACCCCCATGGCCTGGGGTACCAGCTGTGAGGGGAGCTGAGCAGCAGCCACTCGTTCTATGTCCCAGTGCCAGGCTGTACCCTGGCCTTGTCAGTGAGGCTTTCGGGGGCTCAGGAGAAGCAAGGTCAGGTTGGGCGAGGATGTGAGGGCTACCAGCCCTCTGTGTCCAGGGAACAGTGAGTTATCACCGGAGAGAGGCCAGGTCAAGATCTGGTCTGGGATACTGGGTGTCCTGGGTGCTTTCTACTACTGTGGTAAACACCAGGGTCAAAAGCAGCGTGGGGAGGATTAGGCTTGCACATCTCAATCACAGCCCATCCGTGGCAGGAGCCAAGGTGAGAGTTCAAGGCTAGAAGAATCCAGAGGCAGAACCTGAGGCAAACCCTGGAGGAGAACCTGCTTAATGGGTTTCCCCCCCTTGGTTCACTCATTGACCATCTGCCCACGGGTGGCACCTCTCACAGTGGACTGGGCCCTCCCACATTGATATTAATCAAGGAAGTGCTTCCACAGACTTGCCTCCAGGCCAATCAGATGAAGGCATTTCTCTCAGTTAGGATCCTCTTCCAAGAGGGCCCAAACTTGTGTCAGGCTGATGGAAAACTAAGCAGCTCTCAGGGTGTGTGAGGGCCGGAGTCAGGGAGGGACACAGCTGGGCCTACGCTCACAAAGCTAATACTGACTAGAGGCCAGCAAGATGGAGCCATGAGGGGTGCTATGGCCACAGTTCTAGAGAGACTTAAGGTATAAGGCTTGTAGTTGGGGGAGAGAGTGTCAGTAGAAATGGATCTAATTATGGCCCCTTGGGTCACAGCCTTCTTGCCCTATGGTGAGGAAACAGAACAAGACCCAGGCCCTCAGGGCAGGGCCCCAAAGGCTCCTTGAGCCATCTGGCTCTCCAGTACCCTCAGCACCCGGAAGAATCCGACAGTGCCAGCAAGGTCCTTTGCCTCCTTCTGGCTCCTTGAGTCTCCATCTGTCTGTCCGTCTCTGACTACTTGTGGTTTTGCCACACACACTAAACCAACTGGAGAATCAAAATGATTGGTCCAATTTGACCACAACCAGCCAGTGAACCCTCAGATCCAGTTATCTTGACGTGTGTTGTGGCCACACATCTCCATCCACCGAGGGCAACATTACTGAGCTCCGAGTTCCACCCCCTACCCAACCCCGCGCCTCACTTCCGGTTCCTCCTGACGCTTCCGCTCCTTTCTCTGGGCCTCTCCACTCTTCTTTCTCTTACTCTTCCCCCTCACTCCCTTCCTCCTCTCCCCTCTTTGGTTCGGGCTGTCTCTTCTGGGCCTGTTCCCCCTTTTTGCCCCAG
Seq C2 exon
TTTAACTACTACAACTCAGTACTGATCAATGAGAAGGATGACAAGGGCAACTATGTGGAGCTGGGAGCTGAGTTTCTTCTCGAGTCCGACGCCCACTTCAACAACCTGAGGGTGAATGTCTCCATGAGCAGCGTGCAGCTACCCACCAATGTGTACAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008031:ENSRNOT00000010746:4
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:
PF083996=VWA_N=PU(12.0=70.0)
A:
NA
C2:
PF083996=VWA_N=FE(46.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGCCGCTGAGGAG
R:
CACATTGGTGGGTAGCTGCAC
Band lengths:
207-1576
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]