DreINT0071013 @ danRer10
Intron Retention
Gene
ENSDARG00000093411 | gad1a
Description
glutamate decarboxylase 1a [Source:ZFIN;Acc:ZDB-GENE-070912-472]
Coordinates
chr9:3650439-3652205:-
Coord C1 exon
chr9:3652116-3652205
Coord A exon
chr9:3650613-3652115
Coord C2 exon
chr9:3650439-3650612
Length
1503 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CCCTCGTTTTTTTTTTGCAGGTC
3' ss Score
12.46
Exon sequences
Seq C1 exon
CCACAGCACACAAATGTATGTTTCTGGTACATTCCTCCAAGCCTGCGGCTTCTGCCAGATGGAGAGGAGAAACGACATCGGCTTCATAAG
Seq A exon
GTGAGACGATACTCAAAATACTCCCTTCTTTGACGGAGAGTGCTCTTATACTCAAACTATTAACTTATATTTGTGCATATGCCATATATGTTAGCCTGGACCTGGATTATTGTGGGGAATAATCAAAATTACATGAGTGAGTCAAAATTATTCATTTTTCTTTTCCAAATAAAATCATTGAGGGGCGAGGCAGTGGCGCAGTAGGTAGTGCTGTCGCCTCACAGCAAGGTCGCTGGGTCACTGGTTCAAACCTCGGCTCAGTTGGTGTTTCTGTGTGGAGTTTGCATGTTCTCCCTGCCTTCGCGTGGGTTTCCTCCGGGTGCTCCGGTTTCCCCCACAGTCCAAAGACATGCGGTACAGGTGAATTGAGTTGGCTAAATTGTCTGTAGTGTGTGTGTGTATCCCAGAGATGGGTTGCAGCTGGAAGGGCATCCACTGCGTAAAAAACTTGCTGGATAAGTTGGGGGTTCATTCCGCTGTGGCGACCCTGGATTAATAAAGGGACTAAGCCAGGGTAAGGCAAACTTGGTCCTGGAGGGCCGGTGTCCTGCACAGTTTAGCTCCAACACTAATCAACAGGGCCGGAGTGGGACTCCTTTTCAGCCCTGGAGTTTCAAGCCTCAGACCGGCCCACCTCAGTTCACGACTGACTAAGTTATATAAAAATAAGGTCATTCCAATTCAGTTTCTAATGACACTATCATGTCTTTTTGTGAGAAAACACCTGCTTCAGAACTTCAAATGTTCAACAACCCTAACAGTATTATATGTGTTAACAATAAAAATAAAATAAAAAATACATATTTAGACGGGGATCAAACCCGGGTCCATGGCGTCGTAATCTAATGCGATAACCACTGGACCACAACAACTGTATATTGAAAAGTGACTCATATGATTTATATAATCATTAACCTGCAGGCTGGTTATATATAAAAAGAGCAGAGCTGCGGTAAAATAATGAATAAGAAGACTGTGGTCAAGTAAATAAATAAATAAATTTAAAAAGTGTGACTGCTGAGAGCAACAGATTCTGGAGCTAGGGATACCGGCCCTCGTGGCCAAAAAACGGACCGGCCCACCGGGAATTCTCCCGGTCCACCCGAATAGCCAGCTAATCAAACACACCTGAACAAGCTGATCAATGTCTTCAAGAGCTCTAGAAATCTACAAGCAGGTGTGTTTGGTTAGAGTTGGAACAAAACTCTGCAGGAACACCGGCCCTCGAGGATCAAGTTTGCCCATCCCTGGACTAAGCCGACAAGAAAATGAATAAATGAATGATAAAATCATTGGGATGTTAAATAAATATATCAAAATTAAAATTCTTTACCCTCGGATAGCAGATGTTCCTATAGTTTTATCTCAGCCAGATATTATCATATCACAACAAACCATTTATTCAGCATTCAGATGATGTACAGATCTCAATTTCCAAAAATCCACCCTTATTGTTTCGTGATCCACGGTCACACCGTCACATCCCTCGTTTTTTTTTTGCAG
Seq C2 exon
GTCGCCCCAAAGATCAAGGCACTGATGATGGAGTGCGGGACAACAATGGTGGGCTACCAGCCTCAGGGTGAGAAGGTTAACTTCTTCAGGATGGTGGTCTCCAATCCGGCGGTTACCAGGTCTGACATTGACTTCCTGATCGATGAGATAGAAAGACTGGGACAGGATTTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000093411:ENSDART00000140425:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0028214=Pyridoxal_deC=PD(2.7=33.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACAGCACACAAATGTATGT
R:
CTATAAATCCTGTCCCAGTCTTTCT
Band lengths:
264-1767
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]