MmuINT0078378 @ mm9
Intron Retention
Gene
ENSMUSG00000050100 | Hmx2
Description
H6 homeobox 2 [Source:MGI Symbol;Acc:MGI:107159]
Coordinates
chr7:138697576-138700096:+
Coord C1 exon
chr7:138697576-138698088
Coord A exon
chr7:138698089-138698940
Coord C2 exon
chr7:138698941-138700096
Length
852 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TGTTTGTGCTCACTCTTCAGGTA
3' ss Score
9.96
Exon sequences
Seq C1 exon
AAACGAGGAAGGGACATTGGCACCGGGGCTGGGCGGGCTCACCCAGAGCCGGGCCGGCAGGGACCCGCGCACAGCGGTCCGGTGCCTGCGCGTCCTGGAGCAGAAGGGACGCCTCGCCAGCCTCGTAGCCCCCTCCCCTTGCTTTCCCTCCCGCCCCTCCCCCCGCCCGCCTGCCCGCACCACCTTCCACCCAGCCCCGCTCTAAAGGGAGTTCTTGGTTTCCTCCGATTTCTTATGAACCCAGGATGGGCAGCAAGGAAGATGTGGGGAAGGGATGTCCGGCGGCCGGTGGCGTCTCCAGCTTCACCATCCAGTCCATCCTGGGCGGGGGCCCCTCCGAGGCACCGCGGGAGCCCGCCGGGTGGCCAGCCAGGAAACGCAGCCTGTCTGTGTCCTCGGAGGAGGAGGAGCCGGAGGAAGGTTGGAAGGCTCCGGCTTGCTTCTGCCCAGATCCGCACGGCCCCAAGGAGCCAAGCCCTAAGCACCATACCCCCATCCCTTTCCCTTGCCTGG
Seq A exon
GTAAGGATCGCAGGTCGGGAGTCTGGCCCGAGTGAGCGTGAGCCGATGCGGTGTGTGATTGTCGGAGACGCGGAGCAGGGCATCCCCGGGTCACAGCCGGGCCGCTAGTGGTCCAGGCTAAGGGGAGGGGACTACGCACCCATGGTGCATTCTCGAAAAGGCCGGAAGGGCCGGCGCTGGGGAGAAGTAGAGGAATATTGGGGCGGTAAGGGGAAGACTGGGTAAGGGGAAGGAGGGTGAACCAGAGTGGGCCAGGAACTCTGCGGGCGGTACACAATGCTGGCCAAAATGGTTTCGCACGCCGGGTACTTTCTGTCCTGACTTAGTTCTGCAGGTCTGGTTTGGGTGTTCTGTCAGTCCTGCAGGCTCTATGTCTTTTCCCTCCTCTCGGCCTCTTCTCGAAGTGATTAGTACTCTAAAATGATTGACAGTGCTGAGTTTCAGAGAGGTAAAAGCTAACGGAGGACAGCCAAGGAGTTATGAATAAAATTAGCCCGACTCTCAAAGAAAACGGCCTGTAAAATGATGCTACCTTGTAGAGCTCAGTCCTCAAAGGCAAAAATCACCTTTAAAAAATGGTGTTAATGTCCCCATTCCAGACCCGGTACCACGTTTACTTTTATAAGAGTGGAAGGAGACCCTCCAGCTCGGATTATATGGAACCCTCTTCTGCTGCTTTGAAAGGCCGAGGCTCTGGACTTTGGGCGCTAGCAGGACGCAGTAGAAAAGGAAAGGGTTAGCAATAGGGGAATCAAGGATGCAGGCATCAGTCAACCTCCTTGTCCCCGGCAGAGCTGAGAGTCTTTAAGGCTCATCAACTCCATGGTCATTCTGTTTGTGCTCACTCTTCAG
Seq C2 exon
GTACCCCCAAGGGCAGCGGAGGCGCAGGGCCTGCGGCCTCGGAGCGCACGCCATTCCTTTCTCCTTCTCACCCGGACTTTAAGGAAGAGAAGGAGAGGCTTTTGCCGGCGGGCTCGCCTTCTCCGGGCCCGGAGCGGCCACGGGACGGCGGTGCGGAGCGCCAAACCGGAGCGGCCAAGAAGAAGACGCGCACCGTCTTCTCCCGCAGCCAAGTGTACCAGCTCGAGTCTACCTTCGACATGAAACGCTACCTGAGCAGCTCGGAGCGCGCTTGCCTCGCCTCCAGCCTGCAGCTCACCGAGACCCAGGTTAAGACTTGGTTCCAGAATCGCCGCAACAAGTGGAAGCGGCAGCTCTCAGCCGAGCTTGAGGCAGCCAACATGGCACACGCGTCGGCGCAGACTCTCGTGGGCATGCCGCTCGTGTTTCGGGACAGTTCGCTGCTGCGAGTGCCGGTGCCGCGCTCTCTGGCCTTCCCGGCTCCGCTTTATTACCCGAGCAGCAATCTCTCGGCCTTACCGCTCTACAACCTGTACAACAAGCTTGACTACTGACATGCTCGCCCGCCGGCTCCCGGGACGCCCCTGGTCGCCTGCAGCTGCCTGCATAGCCCGGCGCGGTCGGGATCCTTCGCAGAGCTCCGGAGCAGAGCGGCGCGTGTCCAGAAATATTAAGAAATACACCATGTGTATTCGTTATGTCTTATTTATGGCCTCTTTCCTACCTTTTGTTTTGTTTTGTTTTATTTTGTTTTGTTTTGTTTTGAGTATTTATCTGCATTCCTCACGCCAGAGCACCTGCTTTCTACACAAAACCAAACAACTCGCGTTTGAAACTATTTTGGAAGGGGAGGCTCTCGGGTGGTGGTGGGAAGTGGGGTTTTGATTAGGTCGGTTTTGACCAGTAGCAAGAAAAAAAAAAAAACATCAGAAAAACCACCAACAGAACCAGGCAGTCTTTCTCCCATATATACACCTGTATATAGAAAATGTGGTAGGACACAAGCTCAGCCGAGCCGAACCAACTAGGGCTTTGGTCGTTGAACTAATCACTTCTCTTTATTCCCTTCATCTTGAGGATGGGTAGGGGCAAAACGAGGAGAGTACAGATCTGTAAATATTTTTAAAGAGAAAAAAATAAAACGTTTTAAACATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050100-Hmx2:NM_145998:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.978 A=NA C2=0.348
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=30.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGGCAGCAAGGAAGATGTG
R:
CCGGGTGAGAAGGAGAAAGGA
Band lengths:
343-1195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: