DreINT0071012 @ danRer10
Intron Retention
Gene
ENSDARG00000093411 | gad1a
Description
glutamate decarboxylase 1a [Source:ZFIN;Acc:ZDB-GENE-070912-472]
Coordinates
chr9:3652116-3653311:-
Coord C1 exon
chr9:3653204-3653311
Coord A exon
chr9:3652206-3653203
Coord C2 exon
chr9:3652116-3652205
Length
998 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTTTTTAAATTGTGTTTCAGCCA
3' ss Score
8.26
Exon sequences
Seq C1 exon
GGCACTACTGGTTTTGAGAAGCACATTGACAGGTGTCTGGAGCTGTCGGAGTATCTCTACCACAAGATCAAGAACAGAGAAGGATATGAGATGGTGTTTCAAGGGGAG
Seq A exon
GTGAGTGAAAATAATAGCAAACAAAAAGAAAAACAATCAACCTTGACACTGTCAAAGAAGATAATGCACTAATACACACAACAAGACTGGTGACAGAGTGGTTTGATGAACACGAAAGTCAAGCTGAACATCTCCCATAGCCAACACAGTCACCTGATCTAAATATTATTGAGACACTTTGGTGTGTTTTGGAGGAGCGAGTAAGATAATGTTTTCCTCCACCAGCATCACATAATGACCTAGCCACTATTCTGCAAGAACAATGGCTCAAAATCCCTCAGGCCACTGTGCAGGACTTGTATCTGTCATTTCCAAGACCAACTGATGCTGTATTGGCTGCAAAAGGAGGCCCTACACCATACTAATGAATTACCGTGCTCCAGATGTTTTAGTTTCATTTTCCAACCCCTGTATATCCAAGTGAAATTTCTTCCCAAACATGAAGATGAAACACTGCAATCAAACTATTACCATCATTTAGGAATTTTCGCCATATTTTCTGACAAGATCAACACACATGCGACTGTCAGTAAAAGACTGCATATGCACACACATTGCATAATGCAGAGGTATTTTCGTTTCATTAGGCTTGCGTTATAAAACCCCATAACTCTCTCACCAGTCCTTACTCCTTTTTTGCGTCTAAAACCCCTGTTTGTCACGGGGGCATGAAGGAAATGTTCATGAGTTAAAGTGAAACTGCCCAATTACAGGAAACTCTTATATGAAAGCACTTCACATAAACACCTTAACTATATTATTGTCTATTAAGGCAGATAACTAGACTACAGATGTCCATGTAAGCGTAGTCAGTCTTGCCTTCAAAGTAAGTGAAAGATCATCAAAGAATGTAAACACATGCAAGTGCATTGTACCAATTGATAAATTCAAATGGAAGTACATAGTAATTAAGGCCAGTAAATATAAGTATACATTGACTGTAGAATATGTAGAAATATGTTTAATGCATGTATGCTATTTTTTAAATTGTGTTTCAG
Seq C2 exon
CCACAGCACACAAATGTATGTTTCTGGTACATTCCTCCAAGCCTGCGGCTTCTGCCAGATGGAGAGGAGAAACGACATCGGCTTCATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000093411:ENSDART00000140425:14
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:
PF0028214=Pyridoxal_deC=FE(9.3=100)
A:
NA
C2:
PF0028214=Pyridoxal_deC=PD(2.7=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCACTACTGGTTTTGAGAAGC
R:
CTTATGAAGCCGATGTCGTTTCT
Band lengths:
198-1196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]