RnoINT0028183 @ rn6
Intron Retention
Gene
ENSRNOG00000008031 | Cacna2d4
Description
calcium voltage-gated channel auxiliary subunit alpha2delta 4 [Source:RGD Symbol;Acc:1562038]
Coordinates
chr4:151331501-151333673:+
Coord C1 exon
chr4:151331501-151331579
Coord A exon
chr4:151331580-151333539
Coord C2 exon
chr4:151333540-151333673
Length
1960 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
GACAGCCTTGTCCTCTCCAGGTT
3' ss Score
8.9
Exon sequences
Seq C1 exon
GTCCGAGTTTTCACCTACCTTATTGGAAGAGAAGTGACTTTCGCTGACCGCATGAAATGGATCGCCTGCAACAATAAAG
Seq A exon
GTAAATGACTTTGCAGAGCTCTGCAGTCCACACAGAGACAGAGAGATAGCAATGCTGGGCTCCAGGCTTCTGGCCAGAGGCCTCCTCAGGTGCAATACAGTGCAGTCTGTCCCCCATTGTTCAGAGAAAGGGAGGGTGGATTTCTCTGAAGCTGGAGCAGACAATCCATCAACCCCGCAGGGACTCCCGCTTACAGTCATCAGAGATGCAAATCAGAGGCCACTTACACAAGAGAACGTCTCCCCAAACAAAACTTGTACACAGAAGACAGGGTAGGAGGCAAGGAGGGACCCACATTTTCAATGTCTGTAGGCCCTGCCTTTGTTCCTGTTGTGGCAAATTAAGGCATTGACTCTGTTCAAAGGCAAAAGTGGAGGGTCGCCTTTTCTTTTTTCCTTGTGTGTGTGCACACATTGGGGGAACCCGTGTATATGTGTGTGTGCATGTGTGTGGAGGCCTGAGGATTTAAGGAGGAGTTGTTCCTCAGGAGAGGCCATCCATCTTGGTTTGTTTGAAACAGGATTTCTCTTACCCACTGAGCTAAACTGGCTAGCCAAAGAAGCTCAGGGATCTACCCATCTCTGCTTCCTCAGTACTGGATTGCAAGGGCAAGCCAGCACACCCAGCTTTTTTTAAAACATGGATTCTGGGGGTGTGACTCAGGTCTTCATGCTGACTGACCCATTACTCCAGCCCTATTAATCACTTGGTTGATTTTTTTAATTTTATACTTACTTATTCTTGGTGTAAGTGTATATGTGCTGCCCATTTGTGCATGCGCCCAATCACATTCACCTGGGGGTCAGAGGACAACCTGGGAATTCAGTTCTCTCCTTCAATCACAGAGGTTCCAGGGATTGAGCCTGCTAGGTTGTCAGACTTCTTGACAAGTCCCCCTACCCACTGAGACATCCTACCAAACCTATTTATTAGTTTTACAGGACAGGTTATTGCCACACAGCCCAAAACGACCTCAAGTCCTGGGGATCCTCCTGCCTCAGCTTCCCAAGCACTGGGATCACATGTTACCACACACAACGAGTCAGCACTTTCCCTGGAATAATGTTTTCTGTGTTCCAAGACTTCTATCCGGGATCAGAACCCACGACCTGGACTTGCAATGAAATGCTGTTGATTCAACAAAAACTTACTGTGCATGTACTTTGTACCCAGTGCTGTTCGAAGACTGTGGCTCAAGGGTAATGGGACAAATGGCTCAGTCTTGATCTTGGTGTGGCCAGCAGGTGGCCCTCAGTTCCAGTATGGCTTGAATGTGTCATGATGGCACCGAGGCGTGCACTGGACAGGGTGCAGGCTGGGCAGGGTGCAGGCTGGACGGGATGCAGGGACCAATGGGAAAGATACTTTCCCAGTTTGGGGAGCTCGATGAAGGGTCTTTCACATCAAGGGAATAGCGTGCCCTAGGCGTGCGGTGTAGCAATGCTGTCCCATTTTGCTGGCATATGGAACAAATGGCTCCGGGAGGTGGTGGGCAATGAGACCAAAAGTTACTAAAGCACGCAGGGCCTCATTAGCCAGGTGCCCTTCCAACAGTGCTGTGGCTATCCTGAAGAGAATAAAGCAGGCTGCGCCATCACCTGAGGAAGACTGGTGAGGAGGGAAACTAGGAGCTGTGGACTCAGGAGGACAAGAGCTGCCATCTTGTTGGGGTCTCCAAGCCGATTCTCAGAGCGCATACCATGTAGACGACTTGTTGTTGGGCACCACTGCTGCAGCTGAAGCCCCTGCTGTTGTTGAGGGGTGGGATATTAGCATCGAGAAGGTTCCTCCAAGATCCTCCAAACTGGAGCAGAGGCCTGTCTTTGTCTTGTACTAGGAGACAAGGCATGACCTCCAGGAGGGAGAGAGGCCCAGCGAGAAGCACCCAGAAGCTGGGAGTGCACATGACCAAGGAGAGCTTGTCCTTTGCATTCTGTGGTGACAGCCTTGTCCTCTCCAG
Seq C2 exon
GTTACTACACACAGATCTCCACGCTGGCTGATGCGCAGGAGAACGTGATGGAGTACCTGCACGTGCTCAGCCGTCCCATGGTCATCAACCACGACCACGACATCATCTGGACAGAGGCTTATATGGACAGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008031:ENSRNOT00000010746:12
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:
PF135191=VWA_2=FE(14.4=100)
A:
NA
C2:
PF135191=VWA_2=PD(10.6=42.2),PF0274313=Cache_1=PU(8.5=17.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCGAGTTTTCACCTACCTT
R:
CCGGCTGTCCATATAAGCCTC
Band lengths:
213-2173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]