BtaINT0069660 @ bosTau6
Intron Retention
Gene
ENSBTAG00000045812 | GSX2
Description
Bos taurus GS homeobox 2 (GSX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001192200]
Coordinates
chr6:71279032-71280632:+
Coord C1 exon
chr6:71279032-71279608
Coord A exon
chr6:71279609-71280291
Coord C2 exon
chr6:71280292-71280632
Length
683 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGG
5' ss Score
4.66
3' ss Seq
CTCTCTTGGCCCATCTGCAGGGG
3' ss Score
7.64
Exon sequences
Seq C1 exon
ATGTCGCGCTCCTTCTATGTCGACTCGCTCATCATCAAGGACTCCTCACGGCCCGCGCCCTCGCTTCCCGAGCCACACCCCGGGCCAGATTTTTTCATCCCGCTGGGCATGCCGTCCCCGTTGGTGATGTCCATGTCCGGGCCGGGCTGCGCGTCCCGCAAGAGCGGCGCGTTTTGCGTTTGCCCGCTCTGCGTCACTTCGCACCTGCACTCCTCTCGTGGGCCCGCGAGCTCCGGCGGCGGGAACGCAGGGGCCGGGACTGCAGGGGCCGCGGGTGGCGGAGCGGCAGGAGCCGCCGGGGCCCTGCCCTTGCTCAAGAGTCAGTTTTCTTCGGGTCCCGGGGACGCACAGTTTTGCCCGCGCGTGAGCCACGCGCACCATCACCATCACCCGCCGCAGCACCACCATCACCACCACCAGCCCCAGCAGCCCGGCTCAGCTGCAGCAGCAGCAGCGGCCGCGGCGGCAGCGGCGGCGGCCGCGGCGGCCTTGGGGCACCCGCAGCACCACGCACCTGTCTGCACCGCCACCACCTACAACGTGGCGGACCCGCGGAGATTTCACTGCCTCACCATGG
Seq A exon
GTAGGGCGGGTCCTGGGCACCTGCGCGCTACGCCTTGCTGGCTCCCGGGAGTAAAACGTCTCGCCTTCAGTGGAGGAAGTGGGAGCCTGTGGGGTGGGCGGAGGGGGCGAAGGAGGGGCTTTTGGAATAACTGCAGAGTCGTCTCGTAAGTTCCGAGGTGAAAGTTAGCCTTGCCAGACTCTCCAAGCAGCTTGGTGCGCTCGACTCCAGTACCTGGTGTTCGAGTCTGGGATAGTAGAGGGTCCTTTGCGACTTTGAACTTGAAGGCTGAAAAACCGGAGGTTAACTGACTGAGGTCCGGGGTTGGTGTGTTTGAACTGAAGTGTGGCAATCGGGCGTCGACGCTGGCTAAAAGCATCTCGATGCTTTTGGTTAAGCCTGCCTGCCTTTCCGCTAGGGTGGACAGGAGACCGCAGGACTCTCCCAACCCCTCACCCGCCCCCACTTTAATCCTCTGACTTTACATCCCCGAGATCAAAGGCCTTCACTTGCTTTGGGCGTCTCTGTCCTTCCTGGCTAAGTAACTGTTTGTCTCCAAATGAGAAAGAGTGAGGGATGGATACAGGTGTTTGGTTGAGCTTCGCGGGTGGGTCCTTGAGAGGCAGCGTTTCCAAGGGAGGGCCCTGGGATGGGAGCGCCTCGCTGGAGAATTACCTTTCTGCCCTCTCTTGGCCCATCTGCAG
Seq C2 exon
GGGGCTCGGACACCAGCCAGGTACCCAATGGCAAGAGGATGAGGACGGCGTTCACCAGCACGCAGCTCCTAGAGCTGGAGCGGGAATTCTCTTCCAACATGTACCTGTCTCGACTCCGGAGGATCGAAATAGCCACGTACCTGAATCTGTCAGAGAAGCAGGTGAAAATCTGGTTTCAGAACCGCAGGGTGAAGCATAAGAAGGAAGGGAAGGGCACGCAAAGGAACAGTCACGCGGGCTGCAAGTGCGTTGGCAGCCAGGCGCACTTCGCGCGCTCCGAGGATGAGGACTCCTTGTCGCCGGCCTCGGCCAACGATGACAAGGAGATTTCCCCCTTATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000045812:ENSBTAT00000065114:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.518 A=NA C2=0.513
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
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGATTTCACTGCCTCACC
R:
ATCTCCTTGTCATCGTTGGCC
Band lengths:
353-1036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]