HsaINT0073143 @ hg38
Intron Retention
Gene
ENSG00000169840 | GSX1
Description
GS homeobox 1 [Source:HGNC Symbol;Acc:HGNC:20374]
Coordinates
chr13:27792643-27794768:+
Coord C1 exon
chr13:27792643-27793102
Coord A exon
chr13:27793103-27793565
Coord C2 exon
chr13:27793566-27794768
Length
463 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
CTCTGCTCTGCCACCTCCAGACA
3' ss Score
8.18
Exon sequences
Seq C1 exon
GTGGGCGCAGAGGGCGGGCTGGCTGCGGGGCGACCGCGCGCCGGGGCCATGCCGCGCTCCTTCCTGGTGGACTCGCTAGTGCTGCGCGAGGCGGGCGAGAAGAAGGCGCCCGAGGGCAGCCCGCCGCCGCTCTTCCCCTACGCTGTGCCCCCGCCGCACGCGCTGCACGGTCTCTCGCCTGGCGCCTGCCACGCGCGCAAGGCTGGGCTGCTGTGCGTGTGCCCGCTCTGCGTCACCGCCTCGCAGCTGCATGGGCCCCCCGGGCCGCCCGCGCTGCCTCTACTCAAGGCTTCCTTCCCACCCTTCGGCTCGCAGTACTGCCACGCGCCCCTGGGCCGCCAGCACTCTGCTGTGTCGCCCGGGGTCGCTCACGGCCCGGCCGCCGCTGCTGCTGCCGCCGCGCTCTACCAGACCTCCTACCCGCTGCCTGACCCCAGGCAGTTCCACTGCATCTCTGTGG
Seq A exon
GTAAGCGGGGCCGCCGCGCAGAGGGACCGGGCAGAGGTGATCCGAAGCAGGATGGAGAGCCAGAGATGGAGGAAGAGGGACCCTGGGCTTTCTGGGGGCGGTGAGGGTCATGTCGGGGACTAAGGGGGGCGCTTGGGGTGGAGTGAGGATAGAGGGCCGGGACACAACGCCAGGAGGCGGATGAGGGCAGACGTCCAGGTCCTGGAGTGTGGGCCGGGGTAAGTGAGGGCTGGGATCCAAGGCTCTCCATGAAGGGGAAGGGGTTCCAGGGCTGCATGACTCCGGGAGAATCAGGATCTCGGAGCTGGACAAGGAGCGCTCACTGTAGCTCTGCTGTGGATTGTGTTGGGGCGAAGAGATGGGTAAGAGGTCAAAGTCGTAGGATTCTGGCGACCGCCTACCAAGGGATTGGGTCCACAGCACAGAGGTCTGATCGCTTCCTTCTCTGCTCTGCCACCTCCAG
Seq C2 exon
ACAGCAGCTCTAACCAGCTGCCCAGCAGCAAGAGGATGCGCACGGCTTTCACCAGCACGCAGCTGCTAGAGCTGGAGCGCGAGTTCGCTTCTAATATGTACCTGTCCCGCCTACGTCGCATCGAGATCGCGACCTACCTGAATCTGTCCGAGAAGCAGGTGAAGATCTGGTTTCAGAACCGCCGAGTGAAGCACAAGAAGGAGGGCAAGGGCAGCAACCATCGTGGCGGCGGCGGCGGGGGTGCCGGTGGTGGCGGGAGCGCACCGCAAGGCTGCAAGTGCGCATCGCTCTCCTCAGCCAAGTGCTCCGAGGATGACGACGAATTGCCCATGTCTCCGTCCTCCTCAGGGAAGGACGACCGGGATCTTACGGTCACTCCCTAGGCGCGTGTCTCCCTAGGTCGCCCACCCCAAGACCTCCCTGCGCCTCGGAGACTAGTCCTGGGACTCAGCGCTGATTCCCAGGCACCCGCAGCCAAACCACTGCCTGGCATGGATTTGGCACTGCTTTGCAGAGGTCCCGGGCCTGGGCAGGGCTGAGAGCTTGGCAGAGACTGGACCATGGCGTCCCCGCCCCAGGGCTCGCTCGTGTCCAAAGCCAACTCCAAGCTGTGAACACTGTAAGCGCTCGAGTCCTCCTGGGCAGTGCAGCACCGCGGCCCCCGCCCGCAAGCCTGCTTGGCGCAGCGCCTTGCTGGCAGCCGGCGCCTCCTAGCCCGCCCTCTCTGGGCTGGCTTGGGCTTCCTCGCTTACTCTACTCTCCTCCGCTCTCGGTCAAGGTCGGCGGCCTTGGATGCTCGTTCGCTTCTCTTTTTAAAATGTCTTTTTGTCCCTCCCCACCTCTTTCCTGTGATCATTTATTCACTCGGCCCCCGCCCGCCAACACACACATTTATGAACCCCCACTTTTTTTTTCCTTCTCCTTTTCCCTTCCCCTCCTCAGGGAGCCTCCTCCTTCAGTCAGTCCATTTGTCCCTTGATCTGGCCTTGCTGTCCTCAGTCCCCACGGCTCCTCTCACAGATGATAAATTTCGCCCGTAGTATCCATATTGGGGAAACAGATTTGCTCTGTTTCCAACACGCTCTTCCTTCCTCTAAACATAGGACCCCGCTCTGCGCCGCTGGCGACCCCACTCTTCCCCCTCCAGACTCTGGCCCGCCCCAGCCTAGCTGTGTAATTGTACGGCCTCTGCAATGCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169840:ENST00000302945:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.152 A=NA C2=0.496
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=44.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGCCTCTACTCAAGGCTTC
R:
TTCACCTGCTTCTCGGACAGA
Band lengths:
351-814
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development