BtaINT0069659 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009166 | GSX1
Description
Bos taurus GS homeobox 1 (GSX1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105448]
Coordinates
chr12:32445444-32446691:-
Coord C1 exon
chr12:32446368-32446691
Coord A exon
chr12:32445606-32446367
Coord C2 exon
chr12:32445444-32445605
Length
762 bp
Sequences
Splice sites
5' ss Seq
CACGGCCCC
5' ss Score
-16.47
3' ss Seq
ACCACCGCGGCGGCGGCGGCGGC
3' ss Score
-26.71
Exon sequences
Seq C1 exon
ATGCCGCGCTCCTTCCTTGTGGACTCGCTGGTGCTGCGCGAGGCCGGCGAGAAGAAGGCGCCGGAGGGCAGCCCGCCGCCGCTCTTCCCCTACGCGGTGCCGCCGCCGCACGCCCTGCACGGCCTCTCCCCGGGCGCCTGCCACGCGCGCAAGGCCGGGCTGCTGTGCGTGTGCCCTCTCTGCGTCACCGCCTCCCAGCTGCACGGGCCCCCCGGGCCGCCCGCGCTGCCCCTGCTCAAGGCGTCCTTCCCGCCCTTCGGCTCGCAATACTGCCACGCGCCCCTGGGCCGCCAGCACTCGGCCGTGTCGCCCGGGGTCGCTCAC
Seq A exon
GGCCCCGCCGCCGCCGCCGCCGCCGCGCTCTACCAGACCTCGTACTCGCTCCCCGACCCCAGGCAGTTCCACTGCATCTCCGTGGGTAAGCCGCGCGTGGGGGGGAAGGAGGGGACAGACCAAAGTTGGCCAGACGGGGATAGGGGATGAGGACCCTGGGCTCCTGGGGGCGATCATGTCGGGCGTCTGAGGGGGACACTCTGGGTGGCGTGCTGCTGGAGAGCTGGGACTGGACCCCGGCAGGGAGGGAGAGGCAGGAAGTCCCGATCCTAGCGGAAACTTCCAGGAGGGAGCGAGGGCTGGGGCGCAGGGCGTTCCACAGAGTGCGGGGCCCGGTGACTGGTGGAGTACCAGGGTCCCTAGGCTTGGCGAGGAGGCCGACCGCTATTAGCTGCCGTGCATTGTGTTGGGGCGAAGGGGTGGGAGAGAGACCAGAATCCCGGGATTCTGACGGCTGCCCACCGGAGGATGGGGCCCACGGCGCCGAGGTCTGATGGCTTGCGTCTCTGCGCCCCACCCCCTCCAGACAGCAGCTCGAACCCGCTGCCCAGCAGCAAGAGGATGCGTACGGCGTTCACCAGCACGCAGCTGCTAGAGCTGGAGCGCGAGTTCGCCGCCAACATGTACCTGTCCCGCCTGCGCCGCATCGAGATCGCGACCTACCTGAATCTGTCGGAGAAGCAAGTGAAGATCTGGTTCCAGAACCGCCGGGTGAAGCACAAGAAGGAGGGCAAGGGCAGCAACCACCGCGGCGGCGGCGGC
Seq C2 exon
GGCGGCGGCGGCGGCGGGGGCGCGGGGGCGGGCGAGGGCGCACCGCAGGGCTGCAAGTGCGCGTCGCTCTCCTCCGCTAAATGCTCCGAGGACGACGATGAAGTGCCCATGTCTCCGTCCTCTTCGGGGAAGGATGACCGCGATCTCACGGTCACTCCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009166:ENSBTAT00000047372:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.324 A=NA C2=0.623
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTTCCCCTACGCGGT
R:
TCGTCGTCCTCGGAGCATTTA
Band lengths:
342-1104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development