MmuINT0078756 @ mm10
Intron Retention
Gene
ENSMUSG00000038227 | Hoxa9
Description
homeobox A9 [Source:MGI Symbol;Acc:MGI:96180]
Coordinates
chr6:52223100-52227370:-
Coord C1 exon
chr6:52225528-52227370
Coord A exon
chr6:52224483-52225527
Coord C2 exon
chr6:52223100-52224482
Length
1045 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
GTGTCTCTCTCCCTCCGCAGATA
3' ss Score
14.38
Exon sequences
Seq C1 exon
GAAAAAACAGAAGAGGGAAGGATACCAGAGCGGTTCATACAGGGCCCAGAAACTAGGCGAGGTGACCCCTCAGCAAGACAAACACCTCTTGATGTTGACTGGCGATTTTCCCCATCTCCAGTCTGGGGAGCGGGACTAGGCATACAGATGATGGAGCTTAGAACCCGCTGGCTAGGGAATAAAATTCGCTGGGCAGTTTGTGCTCAAAGAAGTGGGCCAGGGCGCTTGTGACACAATCAGGGCGTTTGTGACACAAACCCTTGAGGGTTGGCAGTTCTCTCCTTGGCGGTTGCTCTGGTTGCTCTGTGGGGCCTTCCCTGTGGAGCAAGGGTGATCTGGCCGATGTGCAAGCGCCTGGCTGGCTTTCCAGTCTGACTAGGGTCGGTAGCCCATTTTAGGTGGTTGTATCATCGACGGTGCGTCGCGACAGGGGCGGTGGTCACTCTGTTTGAGGTGGAGAGAGCCTTGTATTTGACTTTTCTAGGCCGGCCCTGGGGGCGCGCGCGGGCGGGGGGCTCACATCTCTGAGGACTGCAAGGATTATTTACAGGGTATTCACCAACCAAACACAACAGTCTAATTTAACCTTTCCAAGTCCTCATAAATTTTTACAGGGAGCCACAGCGAGGCAAACGAATCTGTTGGTCGCTCCTGACTTTCCACCAGCCTGTGTGGCTTCCGAAACAATAACTCCTTATGAAATATCATAAATATAGATTTAAATACAGTAGAGTGAGAATGCGATTTGGCTGCTTTTTTATGGCTTCAATTATTGTCTAATTTTATGTGAGGGGCTCTGCTGGCCGTGCTCACACGCGGGACCCGCGCCTTCCTGATGGCGTGATTAATTGTGATATAAAATAGTCCGCTTAAGAAGTGTGTGTGTCTGGTATGTGTGTGTGTTGGGGGGGTGGCAAGGGAGAGTACAGAGGCAAGGCCAGATTTGATCTTTTAATCTTCGTTGGCCACAATTAAAACAAACCAGATCGTGGAGCTGCGCGATCCCTTTGCATAAAAACATATGGCTTTTGCTATAAAAATTATGACTGCAAAACACCGGGCCATTAATAGCGTGCGGAGTGATTTACGCGTTATTGTTCTGCCGGGCGGACACGTGACGCGCGTGGCCAATGGGGGCGCGGGCGCCGGCAACTTATTAGGTGACTGTACTTCACCCCCCCCTGGTGCCACCAAGTTGTTACATGAAATCTGCAGTTTCATAATTTCGGCGGGTCGGGCTGGGCCGGCCAGGCGCGGGCTACTGCAATGGCCACCACCGGGGCCCTGGGCAACTACTATGTGGACTCCTTCCTGCTGGGCGCCGACGCTGCTGATGAGCTGGGTGCGGGACGCTACGCTCCAGGGACCCTGGGTCAACCCCCAAGGCAGGCGGCAGCTCTGGCCGAACACCCCGACTTCAGTCCTTGCAGCTTCCAGTCCAAGGCGGCGGTGTTTGGTGCCTCGTGGAACCCAGTGCACGCGGCGGGCGCCAATGCGGTGCCTGCTGCAGTGTATCATCACCACCACCACCCCTACGTGCATCCCCAGGCGCCCGTGGCGGCGGCGGCGCCGGACGGCAGGTATATGCGCTCCTGGCTGGAACCCACGCCCGGTGCGCTCTCCTTCGCGGGCTTACCCTCCAGCCGGCCTTATGGCATTAAACCTGAACCGCTCTCGGCCAGAAGGGGTGACTGTCCCACGCTTGACACTCACACTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGCCTTCTCCGAAAACAATGCCGAGAATGAGAGCGGCGGAGACAAGCCCCCCATCGATCCCA
Seq A exon
GTAAGTGTCTCCTTCCTGCAAACCGGCCGCTGCCTCCACGCAGGCCACCAGGATCTACCAGCGCGTCAGCTTTCTCTGGAGCCTGCCTTCGTCCTCGATGGGTGCCTCTGGATCTAGGGTCCGAGAACCAGAAGTTGGTGTTTGGAACACCTCTGATAGGGGCCCCAAGTCCAGAGAACTGTGTGGAGCACCCGGGCCGGCTAGGGGAAAGGGAGGAGGCTGCTGCAGTGAGGGGGCGGGGCGGGCGGGCGAGTAGAGCGGAGACCCGCCGCCCCTCTCCTAAGCTGCCCTGGCCTAGGACAGACAGACTTTGGGCGGTTCTTCGAAAGCAGCGCAGAGAAGTCTTTTGTGCAGCTAGATTGTTCACAAACTGTGGCAGCAACGTCAGTCGGGCAATCTGACCCGGGAAGTTTGGGGAGACCTCAGATTCCCTCCATTTCTTGCTTTTGGAAGGTGGCGGCGGAAATCCTGCCCAAGATGAGGATGCGGGCTTTGGGTCCCTTTGCCAGATTTATTCAAATAAAGTGGAGATGTGATCAAAGGCCCTGGGGCATCCTGCCTTCCGTGGAGTTCCCACGGCCTTCCGGGAAGGTCAAATAAAGAGTGGGGACAGTTGCAAGGAAGCTGGGAAAGGAAGACAGTTGGAGAGAGAGGGGAAGAGAGGGAAAGAGAGAGGAAAAGAGAGGTGGGAGAGGTTAAGCTTGCCACAAGAACTCAGGGCAGCCTGCTCTTTTCTTTGCTGGCAAAAAAAAAAAAAAAAAAAATGGTTTCCAGATTTCATCCTTTCACAATATGCAGACTGTGGGAGGAAGAAGAAGAGGGGAGGACGGGAGAGAGGAGAAAGGAGGGTGGAGATGGGAGGGGGAGCTGAGACTTTCTTGGCTCTGTTGTAAGTGACCCTCCGTGGATCTGTCTGCCAGGGCTTCATTGTGTTTCCTCTAACCAATTCAGCGGCATCCTGCACTTCGGCCAGAGACCCCCAAGAGGCTCCTTCAGACCCTACCGGGATGCTCCTTCTAAACCCAGTGTCTCTCTCCCTCCGCAG
Seq C2 exon
ATAACCCGGCTGCCAACTGGCTACATGCTCGCTCCACTCGGAAGAAGCGATGCCCCTACACAAAACACCAGACGCTGGAACTGGAGAAGGAGTTTCTGTTTAACATGTACCTCACACGGGACCGCAGGTACGAGGTGGCCCGGCTGCTCAACCTCACCGAAAGGCAGGTCAAGATCTGGTTCCAGAACCGCAGGATGAAAATGAAGAAAATCAACAAGGACCGAGCAAAAGACGAGTGAGCCTTTTAGGGGCTCATTTAAAAAGAGAGCAAGCTAGAAAGAAAAAGAAAGGACTGTCCGTCTCCCTCTGTCTCCTCTCCCCCAAACCCAGCCTCCACCCGCACAAAGGGGCTCTAAATCCCAGGCCTCATCTCCCCACTGGCAGTCCGTGCTCAGGCTGGCTCTTAGGCCTGCGGCTTTGATGGAGGAGGTATTGTAAGCTTTCCATTTTATAGAAGGCACACACACACACAAGGGAGGGCATTAGCGCTATTGGCTGTATGTGCTAGCTTGTATATATATATATATATTTAAAAAAAATCTACCTGCTTCTGACTTTAAGCAAAAGGAAAGAAAACTACCTTTTTATATAATGCACAACTGTTGATGACTGGCTGTATAGTTTTTAGTCTCTGTAGCTAATTTAATTTGCTCTTCGTGTGGCAGATCATTCTGCCAAAATACTTGAACACTGTGTTTTATTGTGGTAATTATGTTTTGTGACTCAAACTTCTGTGCTGGGTGAAGTACCCATTGTGATTGTGGAAGCTAGAATTCAATTTGAACTCAGGTTGTTTATGGGGGGAGAGAAGCTGTGGCATAATGTATAGCTCTGTAGTCTTCTGTGTAGCTAGACTGTTAACCTACGATTGTAAACTAGCTGTAAGGATTTCCCAGTGAAATCAGATTTGGAAAGAAAAGAGAGATAGTTCTCCGGGATGCATAGATTCATGATTTATCTACTTTTGAAATGTGGGCTTCTTCATCTTTACGTTCTAGACTCCAATTTTGTCCAATGTATATAGAATCTCCATATTAAAGAAATATTCATAATCAGAAAGCTTGAATATTGTTTTTGCACCAGAGGAGAAGTGAGGAAATTCGGAGCTATACGTGTGTGCAGAGGGTTGCTACCTATGGGTTTACGCTTAATTTTAATTGGGAGAAAGTGAGTGCTTATTGTAATGGAGTTAATTTTATTGATAATAAATTATACACCATGAAACTGCTCTTGGGCTACTGTAGATTTGTATCCTTGGTGAATTTGGGGTTCCCATCGGATTGAACATACACTGTATATTTTGCAATAGTTACCTCAAGGCCTACTGACCAAATTGTTGTGTCGAGATATTTAACTTTTGCCAAATAAAATATATTGATTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038227:ENSMUST00000048680:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.509 A=NA C2=0.354
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.5)
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTTGTGGTTCTCCTCCAGT
R:
TCGTCTTTTGCTCGGTCCTTG
Band lengths:
345-1390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types