DreINT0075668 @ danRer10
Intron Retention
Gene
ENSDARG00000043322 | gsx2
Description
GS homeobox 2 [Source:ZFIN;Acc:ZDB-GENE-041001-114]
Coordinates
chr20:22583375-22584948:-
Coord C1 exon
chr20:22584464-22584948
Coord A exon
chr20:22584163-22584463
Coord C2 exon
chr20:22583375-22584162
Length
301 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TTTTTTCTTCTTTTCAATAGGTG
3' ss Score
11.64
Exon sequences
Seq C1 exon
AGTTTTGAGACCACTGGGCACTGCGCAAGTTCTTGGAGCATCGCCATCAGTGCGGTATCACTGACACCATCAGCATCTCGCTCAGACAGGAGCAATCATGTCGAGGTCTTTCTACGTAGACTCTTTGATTATCAAGGATCCCGCGCGCCCAACTCTAAGCGAGCACACGGCGCAGGACTTTCTCATCCCCATTGGCATGCACTCTCCCGGCGTGATGAGCGTCACTGCGCCCATCTGCCCGTCCCGGAAGACCGGCACTTTTTGCGTTTGTCCGCTGTGCGTATCCTCACACATCCACTCTCCCCGCGGCGGAATTCCACTGCTCAAGGGACAAGGCTTCACTGCCGGTGACGCGGCGTTCTGCCAGAGGATGGCACACCAACAGAGCCCCGCGTTAGCGCACCCTGGACACGGACACGCGCCTGTCTGCACGCCCACAAGCTTCAGCGTCACTGACCCTCGGAGGTATCACTGCCTGTCTCTAG
Seq A exon
GTGAGTGAGTGCGCGCGCGCGCATGCTTATACACCTGTTACTGCTTGTCATGATGCACTCTACTATCTAGCATTAGAAAATTATTAGAAGTCGTTATGCATTGATTTCTCTCTCTGTATCTCTCAGTTACTTTATCTTACTGTGAAACAGATTGAATTGCAGATTTACGCATTTGTACCACGAAGAAAATAAAAACAACTGTTTAATTTTATTTAATTTTATTTATTTATTTTTTTTTTGCGATGAGTATGCTACGCACTTTATTTTACATTGAACTTTTCTTTTTTCTTCTTTTCAATAG
Seq C2 exon
GTGCATCTGACAACAGCCACATACAGAACGGCAAACGGATGCGCACAGCCTTCACCAGCACTCAACTGCTCGAGTTGGAGCGCGAATTCTCATCTAACATGTACCTCTCACGCTTACGCAGGATCGAAATAGCCACATACCTGAATCTGTCAGAGAAACAAGTGAAAATATGGTTTCAAAACCGACGCGTTAAGCACAAGAAAGAAGGCAAAGGTACGCAAAGGAGCGCGCACGCAGGATGCAAATGCTCGGGCAGCCACTCGCATTATCCGCGCTCAGAAGACGAAGAATCCCTGTCACCTGTATCAGCCACAGAGGAGAAGGAGACTTCACCTATTTAGGGGCGTCACAAACATTACAGACTACAATTTTGTACCATACGTGGCACTTTTAAACGGATCGGATGAAACTACTGAGTTTATGGGACGTTGTCTTCTTTCCATAACCCAAAGTGTGTGGAGGTTTAGTCTGTATTCCCACAAACTACTGTTTTACCCTGACACTCAAGTTATATGTGTGTTTTATCAATGTTTCACTGTGACAGAATACTTTTTTTACAGGTTGTTTTAAGTGAATTCTGGTAATTCATTGTCTTCCCTGTTCTTTAAAGAATAAACTTTGGACTCATGAAGAAGATGAAATATTTCCTGTTTGATATTGTAAATATGCAGACTGTTAATCCTAGACTACTGAGAAGCTGTGATTTTTTTTCATCTGAATTTTATGTGCATATTAATGAAAATGTGTATATTTGTATTTATTTAAATAAAAATACATCTGTGACTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043322:ENSDART00000063601:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.540
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGGAGGTATCACTGCCTGTC
R:
GTCTCCTTCTCCTCTGTGGCT
Band lengths:
354-655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]