DreINT0071022 @ danRer10
Intron Retention
Gene
ENSDARG00000027419 | gad1b
Description
glutamate decarboxylase 1b [Source:ZFIN;Acc:ZDB-GENE-030909-3]
Coordinates
chr6:3666931-3668341:+
Coord C1 exon
chr6:3666931-3667222
Coord A exon
chr6:3667223-3668213
Coord C2 exon
chr6:3668214-3668341
Length
991 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGCATATATTCTCCGTGTAGTGT
3' ss Score
6.11
Exon sequences
Seq C1 exon
AACTTCTTGTGTCCGATGGCTTGAGTCCTTAACAATCAACAGAGTCGAGATAAACCCGTGGATCTAAAACCCCTGGACAAATACAGCCGAAGTGATTTTGGAGATTTCTCCTTTACCCCCTCTTTGAAGGATAAACACTGGATCAAGATTTAACGCTGAATGGATTGTTATGCTCTTCCCAATTATTTTGGTTTCCCCATGATAAGAGTCTCGCAGCAACATCACGCGGTGTGAACCATCCTCCGTGTGCCATTTTTACAGGATTTTACTGTGACACCTGTGACTCCGTAAG
Seq A exon
GTAAGCGCTCACCTTCTCTGTTACCATCTAAATTTTCCATGCAGAATTGCGTTTTTGTCTAGTTTTACGATGTTAGGAAGATTATATTTGAAAGAAGAGCTGTATTTTATATATAAATCAGATTTAAATACATATATGTACATATCTAAATCAGTTATTGTGATTATGTGATGATTGGATATGGCAAAATAATGATCTAAAAATATGCTGTAATTTAACACATGAGCGGCGCAATGATTTTTTGCCTATATATTTCGCTCAGTGAGCGATGCTCATTATTTGAGGATATTTAAAGATCATCTTAATTGAGAAATCAATAATTTGCATTTTTTCAATTCATTTTAGCTCTCCCCCTTTCTTTGTGACCTTCTAAAATCACCTCACACAAAAGAAATGTTATTTATCATCGCCATCATTAGACTAAAAATACCGTCAGAAGGATTATTTCTCCTTTGTTATGATGTGGTTGAAGTGAGCAGATTCTTCATTTCTTGGTTTTAAATGATTGGATTTAAAGAGCTCGTTACAGAGCCAATTAAGTCAGACTTCACGGTCTGCTGCGCGCTGGAGCTCAGAGGAGCCGGTGCGTCTGGAGAACACAGCCGGACTGCCATCCTAAATAACAAGTTAGCCTATATAGGTGGGATTATTTCCAGAATTTACTTGCATACGTATTTTATTTTGGATTATTTATTTCCTCTGTTGTGTTTGCTCGCGCTTTTTGGGTGTGCTGTAATGTGCGCTGTTCAATCAGAGCGCATTTCTGAACATGACAGAACACTGAGTGCGCGTAACGCAAGACAAATTATCCTGTGCTGAAGGAGAGTGAATTACAGCCATTTCACAAGGGGAATCTGATGCGTGAAATTATACTTTGGAGAAGAGGAATGATCGCTTTTATAGCTGCATTTGAGATTTAGTCTAATTTTGTGTCTGATTTGTGTCTGCACTTTTTGTTTCTGTCCTAATTCTGCATATATTCTCCGTGTAG
Seq C2 exon
TGTCAGATTTTTCCATTCAGTCTGAAAGCATTGAGGTGTTTCCCGTGGACTGATGGCGTCTTCTGCACCTTCTTCCTCGGCTGGTGATATGGACCCAAACACGGCTAATTTACGACAACCTGCCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000027419:ENSDART00000122348:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.962
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGTGTCCGATGGCTTGAGT
R:
CAGAAGACGCCATCAGTCCAC
Band lengths:
352-1343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]