MmuINT0078379 @ mm9
Intron Retention
Gene
ENSMUSG00000040148 | Hmx3
Description
H6 homeobox 3 [Source:MGI Symbol;Acc:MGI:107160]
Coordinates
chr7:138686477-138688445:+
Coord C1 exon
chr7:138686477-138686876
Coord A exon
chr7:138686877-138687478
Coord C2 exon
chr7:138687479-138688445
Length
602 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
CCGTTTGTCTGTCTCCCCAGCCT
3' ss Score
9.03
Exon sequences
Seq C1 exon
ATGCCGGAGCCCGGGCCGGACGCCTCGGGCACTGCCAGCGCGCCGCCCCCGCAGCCACCGCCCCAACCTCCCGCGCCCAAGGAATCCCCGTTCTCCATCAGGAACCTGCTCAACGGAGACCATCACCGGCCGCCCCCGAAGCCTCAGCCGCCCCCACGAACGCTCTTTGCTCCGGCCTCGGCTGCTGCCGCCGCCGCCGCCGCTGCGGCCGCCGCAGCCAAAGGTGCCCTGGAGGGCGCCGCGGGCTTCGCGCTCTCGCAGGTGGGCGACCTGGCTTTCCCCCGCTTTGAGATCCCAGCGCAGAGGTTTGCCCTGCCCGCGCACTACCTGGAGCGCTCCCCGGCCTGGTGGTACCCCTACACCCTGACCCCCGCCGGCGGTCACCTCCCGCGACCAGAAG
Seq A exon
GTACCGACCTCTCTTTGAACTTTCGTTCTCCCCTCTTTCCCTGTGGGCCGGTCACATTCCCTCTCAGAGATGGTGTCACTGCAGTTAGGGATGCCCCGACACCTGCCAACCAGAGTTTTGGTTAACTTCCTTCGGCCTCTAGCCAGCATCTTTCCTGCGCCGCTCGGCTACGAGGCCAAGGAAACCAATCCCACTTGCTGAGAAAAGAAGTGCAGTTGGAGGCCCGGGCTCTGCGATTCCCGGAAAAAAATTGTCCTCCAGCAGGAATGGGTGGCTTGGGATGGCCTTGGGGGGTGGGGGGGAGGCCTGGAAGGCAGGGTTGAACCTTAGCAGTGGAGAATTTTCCCGCTGGCCCCTGGCGTGGGAAACGCGAGATAAAAGGAGCGGCCCTGATCCCACCATTGCCTGGCCAGTCCTAGAAAGGCGAAGAGATCTTAGATCTTTCTGCCCCACTGCAGCCCAGCGGGGACACGGGAGAACCGAGGCCCAGGGCCAGTAGCCCGAGGCCAACGTGTGGGTTGCGCTTGGTGCTCCCAGATCCCTGCCTCGCTCAAGGCTGTGTCGCTGTGCTTGTGTGTGCGTCCGTTTGTCTGTCTCCCCAG
Seq C2 exon
CCTCGGAAAAGGCCCTCCTGCGAGACTCCTCCCCTGCGTCCGGCACCGATCGAGACTCCCCGGAGCCTCTGCTCAAGGCTGACCCCGACCACAAGGAGCTGGACTCCAAGAGCCCGGACGAGATCATTCTGGAAGAGAGCGACTCGGAGGAAGGCAAAAAAGAAGGCGAGGCGGTGCCTGGCGCGGCCGGGACGACCGTAGGGGCGACTACGGCGACACCGGGCTCAGAGGACTGGAAGGCGGGCGCCGAGAGTCCCGAGAAGAAGCCGGCGTGCCGCAAAAAGAAGACGCGCACCGTCTTCTCGCGCAGCCAGGTCTTCCAGCTCGAGTCCACATTCGACATGAAACGCTACCTGAGCAGCTCGGAGCGCGCTGGCCTGGCCGCGTCGCTTCACCTCACCGAGACGCAGGTCAAGATCTGGTTCCAGAATCGCCGCAACAAGTGGAAGCGACAGCTGGCGGCCGAGCTGGAGGCGGCCAACCTGAGCCACGCCGCTGCGCAGCGCATCGTACGCGTGCCCATCCTCTACCACGAGAACTCTGCGGCCGAGGGGGCGGCAGCGGCTGCGGGGGCACCGGTGCCAGTCAGCCAGCCGCTGCTCACCTTCCCGCACCCAGTCTACTACTCGCACCCGGTGGTCTCGTCCGTGCCCCTACTAAGGCCGGTGTGAGATGGGACAGGGGACAGGGAGTGAGCACCCGGCCACCTTTTGGGGACCCCGGAGGAGACTGGGCCGGGCCGAGGGTGCCGGGCTGTGGCCAGCGACCTTGGGCTCACTGCCTTGCCTCCCACCCCCCAATAGCATTTTGTAAGTATTTGCAATGCATTTTCGTGCAATTAATTCCTATGAATTTGAGGCGCTTCTCCTCTTATTTTTGGTTTTGCTTACCATTGAGAGAAAACGGGGTGGGGCAGGGGGGAACGACAAAATTACCAGGTCAAAACTTCCAATTGAAAGTTCTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040148-Hmx3:NM_008257:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.649 A=NA C2=0.439
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTACCCCTACACCCTGAC
R:
CGGTGCGCGTCTTCTTTTTG
Band lengths:
350-952
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: