RnoINT0068239 @ rn6
Intron Retention
Gene
ENSRNOG00000002266 | Gsx2
Description
GS homeobox 2 [Source:RGD Symbol;Acc:1308047]
Coordinates
chr14:35650985-35652709:-
Coord C1 exon
chr14:35652002-35652709
Coord A exon
chr14:35651326-35652001
Coord C2 exon
chr14:35650985-35651325
Length
676 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGG
5' ss Score
4.66
3' ss Seq
GCTCTCTTTTGGGTCCTCAGGAG
3' ss Score
7.61
Exon sequences
Seq C1 exon
CCCAGTACACCTCAGCATCCCCAAGGGCTTGACCGCCCGCGTACGCACAGCTCTCTGGACAGAGCTCAGATCACGGAAAGAGAGGAGGGGACGCCGCGGCCCGCTGGACAAGCCATCGATCCCCCGTCGAAATGTCGCGCTCCTTCTACGTGGACTCACTCATCATCAAGGACTCCTCGCGGCCCGCACCCTCGCTGCCGGAATCGCACCCAGGTCCGGATTTCTTCATCCCGCTGGGCATGCCGTCCCCGTTGGTGATGTCAGTGTCCGGGCCTGGCTGTCCGTCCCGCAAAAGCGGCGCTTTTTGCGTGTGCCCGCTTTGCGTCACCTCGCACCTGCACTCCTCTCGCCCGCCCGCTGGAGCGGGTGGCGGAGCTACGGGGACCGCAGGGGCTGCGGTGGCGGGCGGCGGGGTGGCTGGAGGCACGGGCGCCCTACCTTTGCTTAAGAGCCAGTTCTCTCCCGGTCCTGGGGACGCGCAGTTTTGCCCACGGGTGAGCCACGCACACCATCACCACCACGCTCCCCAACATCACCATCACCACCATCAGCCCCAGCAGCCCGGCTCGGCTGCAGCGGCGGCGGCTGCGGCGGCTGCGGCAGCGGCCGCAGCGGCGGCCCTGGGACACCCGCAGCACCACGCACCTGTCTGCGCCGCCACAACCTACAACGTGTCCGACCCGCGGAGATTCCACTGCCTCACCATGG
Seq A exon
GTAGGGCGGGGCACCTGCGCGCCTCCGGGGAAACTAACTTTGCTCTGTCAGGGAAGGAGGTGGGAGCCCAGGGGCGGGGTGTGGAGGGAGGTGGGATCTTTTTATGGAACTGTTAGGAGCTTCCCTCAGAAATTCCACGGAGGTGGCGGTTAAGGAGTCAACCTCTTGGCCAGGCCTTGTGCACTTAGCTCTACAGGTGCTCAAGTGTCCTGCGTTATCTGGGCTTTGGGGATCTGGATCAGGACTTCAGAGAAATGGCAGGTTAAACTGACTGAGGCCTGGGGTGGATGTGTTTGAACCTCAGCTTCCCGGTTGGTTAAAGGGTGTCTGCCTTTGGCTGAGGCTGTTAGTTGGTTCGCTTTGCTAGGCTGACGAAGACCGCCGACAAGGGGAAGGAGAAGGGGAAGGGGAAGGGGGAAAGGAAAGGGAAGGGGGAAAGGAAAGGGAAGGGGAGGCAGCTGATGCAAGTTCCACTGGAGTCTTTTAACTTAAAATCCAAGTCATTAAAGGCCTTAATTCTCATGAACGTCTCTCTCACTCCCAGACAGAACTTGGGACGAGCATGGGTGTGCTGGGTTAGACTGGGTTCTGGAGACCCGTTCTTTCCAGGGGTTGTCAAATAGGGTGAAGTCACTTTTTCTAAGGTTTACTTCTCTGCTCTCTTTTGGGTCCTCAG
Seq C2 exon
GAGGCTCAGATACCAGCCAGGTACCCAATGGCAAAAGGATGAGGACGGCATTTACCAGCACGCAGCTCCTGGAGCTGGAGCGAGAATTCTCTTCCAATATGTACCTGTCCCGACTCCGGAGAATCGAGATCGCGACGTACCTGAACCTGTCAGAGAAGCAGGTGAAAATCTGGTTTCAGAACCGTCGCGTGAAGCACAAGAAGGAGGGGAAAGGCGCTTCGAGGAACAATCACGCAAGCTGCAAGTGCGTGGGTAGCCAGGCTCACTATGCGCGCTCAGAGGACGAGGACTCCTTGTCCCCAGCCTCGGCTAACGAAGACAAGGAGATTTCCCCCTTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002266:ENSRNOT00000003080:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.503 A=NA C2=0.504
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
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAAGAGCCAGTTCTCTCCCGG
R:
GAATTCTCGCTCCAGCTCCAG
Band lengths:
352-1028
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]