DreINT0040062 @ danRer10
Intron Retention
Gene
ENSDARG00000026855 | cacna2d4a
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4a [Source:ZFIN;Acc:ZDB-GENE-041210-213]
Coordinates
chr4:20556655-20558526:-
Coord C1 exon
chr4:20558448-20558526
Coord A exon
chr4:20556789-20558447
Coord C2 exon
chr4:20556655-20556788
Length
1659 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TCACTGATGTTTGTAATTAGGTT
3' ss Score
8.3
Exon sequences
Seq C1 exon
GTGCGCGTGTTCACGTATCTGATTGGACGAGAGCTTACATTTGCCAGCAATGTCAAATGGATTGCTTGCAATAATAAAG
Seq A exon
GTGAGACCTCAAGCAATTATTCAGCTTATTTTTGATGCAGTGGCTAGATATTTAATGAGAATGTACGAGACTTGATTTATTAGCTGCTTTAGAGAACTAACTAGAAGAATAAAGTGCAGTAAACAAAAAACTACCAGTGTGATATCAATAAATAACATCACAATAGTACGATAGGAAACACCTTATTAAAACTAACTAAAAATAAAAGATGACTCCAGTATCTAGACACATTAAATTCACAAATGCCCTTTTATGATTCGAAATTAAGCAGAGCATTATAAGCATTATAAGTGTTATTTTTCTATTATTTATACACTGTTATTTATTCATTTTAATTCATATTTTATGCATTTTAATATGTATTTTATGATTTTCCGTTTTTATACACATTTTTATATTTTTAATAAATATATAATGATATTTTTACACACAGATTTATTACTTTTTATTTTAATTGTACTCATTTACTTGAGTACTTGTACTTGTTTTTAGTACTTATTTCAATTAGATGCCAATTTAATGACATTTGGACTTTTAACTTTAATTTTACATTCATTTCTTTTTTATAGTTGGATTAATAATACCAGCAACACAAAGTGCAGTCCATAAAATTGGCAATGAAATTTGCCAATGAAATGTGAAATAAATAAAATGCCAACGAATGAATTGCCAATGAAAGCCAATGTAATTTGAATCTGAATTTAAACAATATCCTACAGCAGTGGTTCCCAAAGTGGGAGTCGCAAGACACTGACAGGGTGTCAATTGATGATTTCCAAAAGTCAAATAAATTTTATTAAACTATTAGAATTACCATATTTTATCCATAACTCACAGAAGACAAAAATAGTAGTTAATAGATACATAAAAAATCATCCTGCAAAAAAAAAAAGCCATCAGCCTTTCAATTAATCTTTTCATAGGATCGATGTGTTTATGTTTGATTAACAACACAGCAATAGCGTCAGCTGCAGCTGCAGCAGATTGATTTTATAGCACTAAATGACACCTTTCTGACACCTTTATGGCAATCAAATACACTAAAAAAGAATTAATGCCACAACTGAACATTGAGAATGGCCTCTGAGTGTTTTTTTTTTTAATTAAACCAAGAATAGACTTGTGCTGGAAACATTGTGCCCACTAGTCTCTTTAGACGCGCTTAATATTAAATTAAACAAATTAATAAATGACTGTATAAATTTTATGGTTGTAAAGACTTTTGCACTTTTTTGTGTTGTCAATATGCTCGTGTTTATTTAAGCCTACTGTTGAGTGCGCAGCATTTGTATACTTATAACTACCTCTGAGGAATGTGGGTGTCGCAAGTCACTGGCATTGATAACCTTTGGGAACCCCTGTCCTACAGTATATCGACAATACAAATTTCCATTTTTTTGGGAACCCCTGTCCTACAGTATATCGACAATACAAATTTCCATTCTTTTTTTATTTTATTAGTTTCCCAAATTTAGAAATAACAATTATTAAAACAGTTAAATATAAAATGTGTAAAAAATTTAATTTCTTAAGATTCCCGAGCCACAACCAGTTCTAATATTATTTTGATTTAATAAGATGAAGTCTATGCCCTCTGCTGGTAGCAGAAAATAAATCAATCACTTTTCTCATTACTATTTCACTGATGTTTGTAATTAG
Seq C2 exon
GTTACTACACTCACATCTCTACACTGGCGGATGTACAGGAGAATGTGATGGAATATCTTCATGTGCTGAGCAGACCAATGGTCATCAACCATGATCATGACATCATTTGGACAGAGGCTTACATGGACAGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026855:ENSDART00000136069:11
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:
PF137681=VWA_3=FE(15.7=100)
A:
NA
C2:
PF137681=VWA_3=PD(3.0=10.9),PF0274313=Cache_1=PU(9.0=17.4)
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:
GCGCGTGTTCACGTATCTGAT
R:
TGTCCATGTAAGCCTCTGTCCA
Band lengths:
206-1865
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]