MmuINT0078747 @ mm9
Intron Retention
Gene
ENSMUSG00000014704 | Hoxa2
Description
homeobox A2 [Source:MGI Symbol;Acc:MGI:96174]
Coordinates
chr6:52112510-52114830:-
Coord C1 exon
chr6:52114265-52114830
Coord A exon
chr6:52113625-52114264
Coord C2 exon
chr6:52112510-52113624
Length
640 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
GTTGGTTTCCCTTTCTGCAGAAT
3' ss Score
8.57
Exon sequences
Seq C1 exon
AATAGTTTAATAGTAGCGCGGTCCCCATACGGCTGTAATCAGTGAATTAGAAAAAAAACACCCCAGCAGCGATCTTCTATGATAGATTTTTTTTTCCTTCGCGCTCGCCTTTTTCCTGGGCCTTGCCCCCCCAAAGCCCCTCCAAAAGAGGGAACTTTTCCTCCGAGGGGGCTCCAAGGAGAAGGCCATGAATTACGAATTTGAGCGAGAGATTGGTTTTATCAATAGCCAGCCGTCGCTCGCTGAGTGCCTGACATCTTTTCCCCCTGTCGCTGATACATTTCAAAGTTCATCAATCAAGACCTCGACGCTTTCACACTCGACACTGATTCCTCCTCCTTTTGAGCAGACCATTCCCAGCCTGAACCCGGGCAGTCACCCTCGCCACGGCGCTGGCGTTGGCGGCCGCCCCAAGTCGAGCCCCGCGGGCAGTCGCGGCAGCCCGGTGCCTGCCGGCGCCCTGCAGCCGCCTGAGTATCCCTGGATGAAGGAGAAGAAGGCGGCCAAGAAAACCGCGCTGCCGCCCGCCGCCGCCTCCACGGGCCCTGCCTGCCTCGGCCACAAAG
Seq A exon
GTCAGTCCGGAGACTTGGCCCCAGGTCTCGGGGACCCTTGTCCCCCTCCGGGCTTCCCTAGGAGCGGTTGTGGGGGAGGGGACCATGAGCTTCGAGGGAAGGGGGAGAGAGAGAGATGCCTGGTGGCGGGTCTCATGCCCCTGTGGTCTCAGGAGTGGGTTTGGTGGAGGGGAAAATAGATCCCGAGTCCCACAATGAGACATATATATTTTGAGGAGGGGGGGCACTTTCCCTAACTTGTGTAATGTAGGATGATTTATTTGAGTTGGAACTGACCTCCTCTTGTCTAGTTGTCCTAGAGTTTGGCTTTTTGACAGTAATGAAGAGTGATAGACCGCTCTTGCTCAGCTAAGCAGCTGATGCATTAATTATAAATTGTGTTGTAGCTAATATAAAGTTTGCTCCCGGATGAAGAGGTTGGGGGAAGCCACAGGCAGGAATTTGATGGAGGTGGAAGAGACTGGGCTTCCCCGGGCTGGGCTCCCAGGAAGGGCAGCACAATAGCTGCACTGCATCCAGGGGCGGCCATTTTGTTGCAGTTGATCTTTTCTGCTGTATTTATGCTCCAATGGAATAACCCTGCTCGGACCCTTCCACCTTCAACTGTATGTGTGTCTCTTGTTGGTTTCCCTTTCTGCAG
Seq C2 exon
AATCCCTGGAAATAGCTGATGGCAGCGGCGGGGGATCCAGGCGTCTGAGAACCGCGTACACCAACACTCAGCTTTTGGAGCTGGAAAAGGAATTTCATTTCAACAAGTACCTTTGCAGACCCCGCAGGGTGGAAATCGCCGCGCTGCTGGATTTGACCGAGAGACAAGTGAAAGTGTGGTTTCAGAACCGGAGAATGAAGCATAAGAGGCAAACCCAGTGCAAGGAGAACCAAAACAGCGAAGGGAAATTTAAAAACCTGGAGGACTCGGACAAAGTGGAGGAAGACGAGGAAGAGAAGTCACTCTTTGAGCAAGCCCTCAGTGTCTCCGGGGCCCTTCTGGAGAGGGAAGGGTACACTTTTCAGCAAAATGCGCTCTCTCAACAGCAGGCTCCCAATGGACACAATGGCGACTCCCAAACTTTCCCAGTTTCGCCTTTAACCAGCAATGAGAAAAATTTGAAACATTTTCAGCACCAGTCACCCACTGTTCCTAACTGCTTGTCAACAATGGGCCAGAACTGTGGAGCTGGCCTAAACAATGACAGTCCCGAGGCCATCGAGGTCCCCTCTTTGCAGGACTTCAATGTTTTCTCCACAGATTCCTGCCTGCAGCTTTCAGATGCACTGTCGCCCAGCTTGCCTGGCTCCCTGGACAGTCCTGTAGATATCTCAGCTGACAGCTTTGACTTTTTTACAGACACACTCACCACAATCGACCTACAGCATCTGAATTACTAAGAACATTAAAGCAAAACAAAGCTTCACAAAACAAAACGCCTTTGACCAGGTGGCTTTGCCTTCTTTTATTCTGGGAGTTGATTTTCGTTTTAGTTTCTTCTTGATCTACCCCTACTCTCTCAAATGTTGAGGACTTTCCGTTTAATGTTCTCCCCTGACACAGTTTTAAAGCCATCTCTTGCAAATTATGTTGGCGTTCTAAGTGGTTTTTACACAGAACCCAACAAGCTTCTATGTGATTTTCCTGAAAAACAAAACAGGAGGCCTGCAAGAAAGTGACCATAAATTGTCTTGTCACTTTCTGTTTATTTTTGTACCACATTAGAATGCATTGTCATGCGTATTTTTGGTAGAATAAATTCTCCTTTGCTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000014704-Hoxa2:NM_010451:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.756 A=NA C2=0.516
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGAAGGAGAAGAAGGCGGC
R:
TGTCCGAGTCCTCCAGGTTTT
Band lengths:
356-996
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: