DreINT0040095 @ danRer10
Intron Retention
Gene
ENSDARG00000023886 | cacna2d4b
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4b [Source:ZFIN;Acc:ZDB-GENE-100422-18]
Coordinates
chr25:18962420-18963273:-
Coord C1 exon
chr25:18963115-18963273
Coord A exon
chr25:18962495-18963114
Coord C2 exon
chr25:18962420-18962494
Length
620 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CTAATGATGGTGTCGTTTAGCTT
3' ss Score
2.77
Exon sequences
Seq C1 exon
GTGTTCAAGAGCAAGGCTCACAGTCTGCTGTTCATGACGTCGGTGGCCATGCCAGTGTTCAGTAAGAAGAAAGAAACACTTTCTCATGGCATTTTGCTAGGTGTTGTGGGAACTGACATCCCCCTGCTGGAGGTCATGAAACTTGCCCCGCGATATAAG
Seq A exon
GTAAAAGAACACCGCTAACGCCAAAACTTTTTTAATTTAGGTCAAATATTAATATATGTATACATGTCATTTAAAAAAAAATATTTAAAAATTTCAAGGGGACTTTTATGTTTTTGCATGTATTTTATTCATTTTAAATGTGTAATAAATAACAATGTTTGTGAAGTACAGTAAACGTGTGATGAAAACAATGGAAATGCAAAAATACATGTATACAATTAAACACATTTACATTATACAAATTAAATAATATCTTAATCAAATTATGTTTAATTATTACATTTCATAGTTATTACTTAACATGTACACATAAATACACACAAAAAATAACTAATTTATGTATATTTTCCATTACTTGCTTGTATTTTTATGCCCCTTTAGAAATCAAATGTAAAATAATATTTTATTATTATTACAATATTGATATTAATGGAGATTTATACCATTTAAATTATGCGACCATAAGAAATAAAATCTATTTAATTACAGTTTAAACATATTAATATATTAATTTTGGCACTTTTATGTAACAAATGTGACTTTTTAAATGTTTAAATATTATAAGACAGAAAAAGACTGTGTAAATGTGAAATTATAAATCTAATGATGGTGTCGTTTAG
Seq C2 exon
CTTGGAGCACACGGCTACGCTTTCCTCATCACAAACAATGGCTACATCCTGGCACATCCTGACTTAAGACCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000023886:ENSDART00000027465:14
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:
PF0274313=Cache_1=FE(55.3=100)
A:
NA
C2:
PF0274313=Cache_1=FE(25.5=100)
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:
AGCAAGGCTCACAGTCTGCT
R:
TGGTCTTAAGTCAGGATGTGCC
Band lengths:
222-842
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]