DreINT0075667 @ danRer10
Intron Retention
Gene
ENSDARG00000035735 | gsx1
Description
GS homeobox 1 [Source:ZFIN;Acc:ZDB-GENE-041008-135]
Coordinates
chr5:67231933-67233400:-
Coord C1 exon
chr5:67232937-67233400
Coord A exon
chr5:67232848-67232936
Coord C2 exon
chr5:67231933-67232847
Length
89 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TTTTGTTTATTGTTCAACAGAAA
3' ss Score
8.63
Exon sequences
Seq C1 exon
ACCATTCTGCCATCCAGCATTTGGTACACGAGCGAGACTGAAACTTTCTAACAGACATCAGGTGAAGACACACGGCGCTGTCAAGATGCCAAGATCCTTTCTTGTGGATTCCTTGATTTTGAGGGAGAACAGCGAAAAGGGCACAGAGAACAGCCCTCCGTTATTTCCGTACGCGGTGCATCCTTCTCATCCTCTCCACAGCCTCTCCGCCGGCTCCTGCCACTCTCGAAAAGCGGGTCTGCTGTGCTTTTGCCCGCTGTGCGTCACTTCTCAGCTTCACCCATCTCCCCCAGCGCTGCCCCTCATCAAGGCTTCATTTCCAGCGTTCGGCACCCAGTATTGCCACTCCGCGCTCTCCAGACAGCACTCCACATCCAGCGGCGTAAACCTCAACAGCGGCTCTGGCTTATATCAAGCCGCTTATCCGGTTCCAGATCCACGACAGTTCCACTGCATATCCATAG
Seq A exon
GTAAGTGTGTCATTTGTGCATTGAAAAAGTTTTGCAATTAAACTTTTTATGTATATCAGCAACTTAACTTTTTGTTTATTGTTCAACAG
Seq C2 exon
AAAATAGCAGCAGTCAACTTCAGAGCAGCAAACGCATGCGCACTGCGTTCACCAGCACGCAACTCTTGGAGTTGGAAAGGGAGTTCACCTCCAACATGTACCTGTCGAGACTTCGGCGCATAGAGATCGCAACTTACCTCAATCTATCCGAGAAGCAAGTCAAGATTTGGTTCCAGAACCGCCGCGTAAAGCACAAAAAAGAAGGCAAAAGCGGCTCCCACAGAACGGGCGCGCACAACTGCAAGTGCTCATCCTCCCTGTCCTCCGCCCGGTGCTCCGAGGAAGAGGATGACCTCCCAATGTCTCCCCCGTCATCAGAGAAAGAGGACGCAGACCTGTCCGTCAGCCCGTGAACATGACCATCACCTCAAAAGACTCTGTACGCCACACCTGTGGAATCTTGAATGCAGCCAAAAAGCGACGGCATCTGCGCGCGCCGTCACCTGTACATAGCGAGAAAGGAAGAAACAAAACTTTATATATGTTCGGGGTCTGCGTATCCCTTTTAATGTTGTACATTTGTATACATGTTCAATGTTTGTAGTTTTTTTTCTGAAAACAACTTGCTGATAAGCCCATAGTTCTGCATCCAAATATGATTCCTGTCACCAAAAGGTTTTTAAAAATCTGAGCGGTCCAAAACGAACAAAAATATTATATTATTTACCTACTTTTTAATTTCTATTTGTATTTTTTTATATATGCATATCCAGAACTGTTTGGTTTTGTTTTGTTTGTATGGTGAGTACAGGGTAGCTTTAAGCACATTTTGGTGACAGAATGGAGATATGGGATGTATCCGATGTATACGTCACTTCGATGACAGAATTTGTTATTGTACTTTTATTGTAATGAGAATATTTATTTATTTAAAAAACATTAATGCTGAAAATAAAGAATATTTCTTAGTGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035735:ENSDART00000051833:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.063 A=NA C2=0.320
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=48.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGATCCACGACAGTTCCA
R:
AAGTTGCGATCTCTATGCGCC
Band lengths:
170-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]