GgaINT0120291 @ galGal4
Intron Retention
Gene
ENSGALG00000013007 | CACNA2D4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:HGNC Symbol;Acc:HGNC:20202]
Coordinates
chr1:61179339-61181411:-
Coord C1 exon
chr1:61181314-61181411
Coord A exon
chr1:61179433-61181313
Coord C2 exon
chr1:61179339-61179432
Length
1881 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TTGTTCACCTTCCTCTGTAGGCG
3' ss Score
10
Exon sequences
Seq C1 exon
GATTTACTGCATCACAGACATCGATCCAGACCACCGGAAGCTCAGCCAGCTGGAGGCTGTGATCCGTTTCCTCACGGGAGAGGAACCTGACCTGGAAT
Seq A exon
GTAAGTTCTCACCATCCCAAAGGCCCTGCTGGGTTCTCCTCTACCTGCCACAGGGGAATGAGAACTGTGAAGCTGATTGGTGTCAGACTGAGTTTCTGAGGCACCTGTTCATGCAGGCAGGGCTAAACCTAAGCCTAGCTTAATCCACAAGTGGAAACAAGCTGAGGATCCGCTTCCTTGTCTTCAGTAGAGAATTTTTTTTGCCATTTCAAAGCTGTTACATAACTTGGCTTCACTGAGATCTTTACATAGGTAACAGTGAAGGTCGAGAGGCTTGAATAGGAATGTGGTGGGGGCTGAACACCTTGTTTGAGACTAGAAGGGCGATGGCAGGAGGAGCAAGAAAGCTGCTGTGGTTATTCTGCTCCCCAGAGCTCCAGCTAGCATCCTCCGAGGGCTGCACTGTGCCATGGAGACAGATGATCTCTCTGAGAAACGTTACTAATTTTTTTTCCAAACACAATTTGTAATTGATTTGAGGGGGAAAAAAATGTTACAGAATGATTACCTTCCTTGCTGCTCATCCCTTGCAACAGGTCTGAATCTCCATGTGAAATGCAGCCACATAAGCAGCTGATGTAGCACCACTACAGAGTGAGAACTCTGCTGGTAGGCAGAAGTGGGCAGCTGTGCATGGGATCTCCCAACAGCACTTTAGCTTTAGGATGTCCTTCAGTCCACCCCACTCTCCATGGCTTCAGCCTTCTTAGTTATGCAAAGTGCTGAATCAATATTTTGTATGTAATGCTTCAGAAACCTCTGATACAAGGATTTCAAGGATTTGAGTCTCTTAAAACTAAACCTAGACATAATCTGTAATCTGATAATTGCTCCTCTCTTATACTGTGTGAACAGACCCCTCCTGGCTTTATTTAGAGAAGGCTGAAAAGAGATGTAGCAGCTGAAGAGGCTGGGAAGAAGGAGGAAAGTTTTGGGAGAGCTGACTGGGAGAAGCATGCAGATTGGAAGTGCTGTGAGAGAAAAAGAAATAGGACTAGGATGCAACCTAGGCATGTGGGGCCTGAGGAAGGAAAGATCAGCTGGTGACCTCTGACTTTGAGTTCTGAATGACAGGAAGATGGAGAAATGTATCCTGCCAGCTGTGATAAAGAAAGATTAGGAGATACCTGGAGGCTCAAGACAGAATATGAAGCCAGAAGCATGAAATAGAGGGGATGGCTCTGCCTAGAACAGCATCGGAAGGGCCACATCTGCAATATGATAGCCATCACATCCTCATGCCATGAGACAAATGGAAATAGGGCAGCATAGAAATGAAGTAGGTCAAATAAATGGGATTTTAGACTATACCATTTAGTACATAATGATATCTCAAACTTTTCTAAATATCTTTCAGACCCAATGCAGACTGGACTGAACTGGTAATCTAGACTGGTCAAGTGTCTGGACAGGAAAGCATTTTGTGAGATTCACAGTAAGGACAGGTGGTTAACTAAAGGCCATCAAGAAGTCACTAGGGACTCTGAAGAAATCTTGGGAGGAATGGAGTGGATGGTATCCTCACAACAGGGCACCCAGAAGGAAGGTTAAGGCAGGGATCTGAGGCAAAGCCTGATGAATAACTTCATTTGAAAGCTTCTCATTTGCTTACACTTTCAAACCTAAACCCTTCCATTCAGCTTGCGGGGGAACCAGTGTTATGATCTGAGCTGTAACACCTTGTCCTGTGCTCTTCTACATCTCTCCATCAATCCATCTAGGATTGTAGGTCATGTTTTCAGTCCTACAAATGGAGGGCTCATTTGTGCCTGTTGCTCCACTGCCCTGGGTCAGGCAGATGGTCCACAACGAGGAACTCTCTGAGACATCTACAGGGACACATGTCTTTCTTTTCTGACTCTTGTTCACCTTCCTCTGTAG
Seq C2 exon
GCGATGAGGAGTTGGTCCAGGAAGTGCTGTTTGATGCAGTGGTCACTGCACCCATGGAAGCCTACTGGACAACACTAGCCCTCAATATGTCCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013007:ENSGALT00000037501:22
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCATCACAGACATCGATCCA
R:
GTGGACATATTGAGGGCTAGTGT
Band lengths:
185-2066
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]