DreINT0071030 @ danRer10
Intron Retention
Gene
ENSDARG00000027419 | gad1b
Description
glutamate decarboxylase 1b [Source:ZFIN;Acc:ZDB-GENE-030909-3]
Coordinates
chr6:3668214-3670107:+
Coord C1 exon
chr6:3668214-3668341
Coord A exon
chr6:3668342-3670044
Coord C2 exon
chr6:3670045-3670107
Length
1703 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
CTCCAAACGTCTCGTTTTAGCCT
3' ss Score
4.82
Exon sequences
Seq C1 exon
TGTCAGATTTTTCCATTCAGTCTGAAAGCATTGAGGTGTTTCCCGTGGACTGATGGCGTCTTCTGCACCTTCTTCCTCGGCTGGTGATATGGACCCAAACACGGCTAATTTACGACAACCTGCCACAA
Seq A exon
GTAGGTCTCTCTGGATAACGCGTTTTTCACTTGGCTTGTTTACTCCGTGGGGTGGCGATGTTCATCACTGCCTTAAAAAACACACCGCACCGTGTGAAATGTCTATTAGCTGACAGATCACCTTACAGCTGGAGAGACGAATCATAAATTATCATAGATAGACAGAAATGCTGGGTTGTTTTAACCTAGCGTTGGGTCAAATGTGGACAAACTCAATGTCGGGTTTTTGAAATGCGCACGTTGGTTCATATTTGACCAAATGCATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATTTTAATAAAGATAATAAGTTTTTAATAAAGGAAGATCAATAGATAGATGATGTATAAGACAAAATTGATCCCTTATTCTATTTTGCGGTGTATATATTTGTCTTAATTCATACCAGAAGATTTAAATAATAACAAAAAATGTTACCATCATTTTGTGTACGTTTTGCATTAAATTGGGATCCCGTTTTTATAACAATGGTGCTGCTTGTTGGCACGTTTTATGGTGGCTTAAATAACAGCAATCAGCCATCATCTGCTTTCAACAGTCCCACCTCAATAGCGTAATTACCTAAAATTACCCGCCATTACGCTCCACTTCACGTTTTCCTTTGTAAATATGCTAAAATGGCCAAGTCAAGATCTTAAAATGCATTAAAAATTAGTTTGATGTTATATAATATATATAACCTTTATGTGCTTTTGTGTAGATTGTGATAAATTAAAAATATCATGCTTAATGTAATGTATTGTATTGATCTAGTAAAAGCTATATATGGGTTTTTTTCCATTTTATATGCTGTAAAAAATTGTGCTGCTGTGCTGTGTGTGTGTGTGTGTGTGTATTCTGCGTGTTTTGCTATTATCTCCCTGCCAAGCTCTATCTCACGCTTACTGACCTGAGGGGCTCGTGCTGTCTGTGCCTCATCCTGACAGCGCGCGCCTGGGGCAAATAAAGCCAGATCTGCCCTCAGACAAAACCCACCCAGAGCATGACATCAATTTATATCAAACTATTAATAATTATTATATACATCCCCTGCTTCGATTGGAATCGCTTTATCATTCAAAGTCATACCTATAGTATTTAAATGCAATGTCAAAATGTTTTGCTGAATTATGCAAATGCTTAACGTTGTGATTGTGCGTACATTTTTCTTGCATCGACATTGTAATGCTGCATCTGTCTGGTCACTAACGCCTGGAGGTCATTCATGTGTATATTCCGAATGGTCCATTTTCTGTAGACTCGCTGTATATGACGGCTGGCAAGTCAAACACAAGCGATTCACTCAATTAATCCCGAGACCTCATTTCATGCCCGCTTATTTTAAACCGCCTCTTTGCCGGATGTGTGCCACCATCTATTAGCTGCCTGCCTCTCTGATAGCCTCTATTGATTGCTTGAGGGAAAATCAAGCTCTTTGAAAAAATCTAGGAAAAAGGCACAGAGCCTGTAAAGATGTGTTGCACACATTCATTGTGTTTTGCGTCAATGCATGTTGCACTTTGCGCTTTTACACAGGCGCTCACATCCTCACCCATAGCATAAAAGCAATTACAAATATGGGATGTTGAACAGCTCTCCAAACGTCTCGTTTTAG
Seq C2 exon
CCTCGGACGCGTGGTACGGGGTTGCACACGGATGCACGAGGAAACTGGGCATGAAGATCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000027419:ENSDART00000122348:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.962 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
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:
TGTCAGATTTTTCCATTCAGTCTGA
R:
ACAGATCTTCATGCCCAGTTTCC
Band lengths:
190-1893
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]