BtaINT0072831 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017911 | HMX2
Description
H6 family homeobox 2 [Source:HGNC Symbol;Acc:HGNC:5018]
Coordinates
chr26:43270656-43272421:+
Coord C1 exon
chr26:43270656-43270923
Coord A exon
chr26:43270924-43271864
Coord C2 exon
chr26:43271865-43272421
Length
941 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TATCTGTTCTCACTCCCCAGGTA
3' ss Score
11.47
Exon sequences
Seq C1 exon
ATGGGCAGCAAGGAAGATGCGGGCAAGGGGTGTCCGGCGGCCGGCGGCGTCTCCAGCTTCACCATTCAGTCCATCCTGGGCGGGGGCCCCTCGGAGGCGCCGAGGGAGCCGGCCGCCTGGCCGGCCAGGAAGCGCAGCCTGTCCGTGTCCTCGGAGGAGGAGGAGCCGGACGACGGCTGGAAGGCACCCGCCTGCTTCTGCCCAGACCCGCACGGCCCCAAGGAGCCCGGCTCCAAGCACCACCCCCCCATCCCCTTTCCTTGCCTGG
Seq A exon
GTAAGGATCGCACGCCGCCGGGTCGGCCTGGAGCAAGCTCTAGGGGTGGGAAACTGTGCCGGGGCTCTCGCGTCGGGCCCCCCGCCCCCGGCCAGAGCCGCGGCCGCGCGGGGTCCGGGGCCGAGGGTGGGGTTGGGGGGAGAGGCGTGCTCCGCGCTGACTCCTCCGCCCCGCGGGTGCTCGGGAAGAAACCGGGAACACAGATGCCGCGCGGCGCGGTTTGGGGGAAGGTTGGGTTGATGGGAGTGTATTTGTGGGTTTGGCACAGGGCCGGCCGCTCTCAAGGCTCTGCAATATCCCCTTTGCACATCGGATACTTTCTGCACACGATGTCTGGAAGTCGGATCTGAGCGGTCCGCCCGTCCGTCTCTACCGCAATCTCCTTCTGCGTCCTTTTCTTCTCTCTCTTCCCCTCTCTTCGACCTCTGCCTCTCTGTCTCCCCTCCTCCTCCTCAGAATGATTAGCACTCCAAGATGATTGACAATGGTGCCTTTCAGAGATGGTTCCTCTTTACAACATCTGACCAAGGGGAGCCCCGTGTCAGTCCTTAGCGTGATTTCCGAACAAATGGCCTGTGAAACGATGCCACCCTATAAAGCTCAGGGAACTCTTCCAGCTCAGTTACTACAAGGCAAAATCTTTTAAAAAGATGCTAATGTTCCCCCTCCAGACCTCCTCCCCCTGTTGCCACACGTCCTTTCAGGAAGCTGGGAGCACAGAGACCCCAGGCTCCAAGTAGTTGGGTCCCTCTCCTGTTGCTTTTCAAAAGCCGGGTGCCGCTTTTTGGGTTTCAGCGAGAGGTCGAGAAAAGTAGGGGCTGAGATCCAGGAAGATGGGAACCAAGGCTGCAGGCGCCAGCCAAGCCCCTGGTCCTGGCAGGAGCTGGGGGTCCATGAGGCTCCCCAATTCCATGGCTCTCTTATCTGTTCTCACTCCCCAG
Seq C2 exon
GTACCCCCAAGGGCAGCGGAGGCGCGGGGCCGGCGAGCTCGGAGCGCAAGCCTTTCCTTTCTTCTTCGCACCCGGACTTTAAGGAAGAGAAAGACAGGCTCTTGCCCGCGGGCTCGCCGTCGCCGGGGCCCGAGCGGCCGCGGGACAGCGGCGGCGCCGAGCGGCAGGCGGGCGCGGCCAAGAAGAAGACGCGCACGGTCTTCTCGCGCAGCCAGGTGTACCAGCTCGAATCCACCTTCGACATGAAGCGCTACCTGAGCAGTTCGGAGCGCGCCTGCCTCGCCTCCAGCCTGCAGCTCACCGAGACCCAGGTCAAGACTTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTCTCCGCCGAGCTGGAGGCGGCCAACATGGCGCACGCGTCGGCGCAGACTCTGGTGGGCATGCCGCTGGTGTTCCGGGACAGTTCGCTGCTGCGCGTGCCAGTGCCGCGCTCGCTCGCCTTCCCCGCGCCGCTCTACTACCCGGGCAGCAACCTCTCGGCCTTACCTCTCTACAACCTCTACAACAAGCTCGACTACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017911:ENSBTAT00000023806:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.351
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=30.6)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCCCCTTTCCTTGCCTGG
R:
ACCAAGTCTTGACCTGGGTCT
Band lengths:
344-1285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]