RnoINT0068238 @ rn6
Intron Retention
Gene
ENSRNOG00000000952 | Gsx1
Description
GS homeobox 1 [Source:RGD Symbol;Acc:1310020]
Coordinates
chr12:9605873-9607168:-
Coord C1 exon
chr12:9606760-9607168
Coord A exon
chr12:9606250-9606759
Coord C2 exon
chr12:9605873-9606249
Length
510 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
GCCCCCACGTCGCCCTCCAGACA
3' ss Score
5.83
Exon sequences
Seq C1 exon
ATGCCGCGCTCTTTCCTGGTGGATTCCCTTGTGCTGCGGGAAGCCAGCGACAAGAAGGCTCCGGAGGGCAGCCCGCCACCGCTCTTCCCCTACGCGGTCCCCCCGCCGCACGCGCTCCACGGCCTCTCGCCGGGCGCCTGCCACGCGCGCAAGGCCGGCTTGCTGTGCGTGTGTCCCCTCTGTGTCACCGCTTCGCAGCTGCACGGGCCCCCCGGGCCGCCGGCGCTGCCGCTACTCAAGGCGTCCTTCCCTCCCTTCGGATCGCAGTACTGCCACGCACCCCTGGGCCGCCAGCACTCTGTGTCTCCCGGAGTCGCCCACAGCCCGGCCGCGGCTGCAGCAGCTGCCGCACTCTACCAGACCTCCTACCCGCTGCCGGATCCCAGACAGTTTCACTGCATCTCCGTGG
Seq A exon
GTAAGCGGGGTCCCCGTGCGAACTTGTGGGGAGGGGTGATCTCAGTGGGGCAAGTGAGCGAGCTAAGGATGGGAAAACGGCGCGCTATGGGGCCGGTGAGGATACTTGAAGGGCGCTCACAGTGCTAGACTGGGACTGGACGTAGGAACCGGGGAGAAGACTGAAGATCCTGGGTCTGGGGCCAAGGGGAAGTGGTTGAGTTAAGGTCAGCTTCGGTGAGTTCCATAAAGGGGTGTTATTAACAACCGATTCGGAGGAGAATTGGGGAGTCTGTGACTTAGCAAGGAGGCACTCGCCTGTGGAGTGTAGTGAGGGGAAGGGGCGTGTGTCTTGAGTCCAAGATTGAAGCTAGCTTCAGTTCAGCGGGAAATTAGGCCCACGGCTCAGAGAGGTTTGATGATTCATTCTCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCCCTCCCTCCCTCCCTCCCCCTGCCCCCACGTCGCCCTCCAG
Seq C2 exon
ACAGCAGCTCGAACCAGCTGCCCAGCAGTAAGAGGATGCGGACGGCGTTCACCAGCACGCAGCTCCTGGAGCTGGAGCGCGAGTTCGCCTCCAACATGTACCTCTCCCGCCTGCGGCGCATCGAGATCGCGACCTATCTGAATCTGTCCGAGAAGCAGGTGAAGATCTGGTTTCAGAACCGCCGGGTGAAGCACAAGAAAGAAGGCAAGGGCAGTAACCACCGCGGCGGAGCTGGGGCGGGGGCCGGCGGGGGCGCACCGCAAGGCTGCAAGTGCTCTTCGCTCTCCTCAGCCAAATGCTCAGAGGATGACGACGAATTGCCCATGTCTCCATCTTCCTCCGGGAAGGATGACAGAGATCTCACAGTCACTCCGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000952:ENSRNOT00000001260:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.146 A=NA C2=0.456
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=45.2)
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
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTCAAGGCGTCCTTCCCTC
R:
TCTTCACCTGCTTCTCGGACA
Band lengths:
342-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]