MmuINT0078788 @ mm9
Intron Retention
Gene
ENSMUSG00000042464 | Hoxd4
Description
homeobox D4 [Source:MGI Symbol;Acc:MGI:96208]
Coordinates
chr2:74563520-74565762:+
Coord C1 exon
chr2:74563520-74564035
Coord A exon
chr2:74564036-74564932
Coord C2 exon
chr2:74564933-74565762
Length
897 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TTCCTTATTTTGCACCCCAGTAG
3' ss Score
4.56
Exon sequences
Seq C1 exon
CTCGACAGTCTCAGCCCAGGGAGGCTCGGTGGCCGCAAACAGCGCCTGCCTCCGGGTCTGCAGCAGCAGTCATAGCAGCAGCAGAAGCAGCAGCAGCGGGATCCGAAAGTCCGGCGGGGCTGAGGGCCCAGAAAGGTAAATGCTCGAATTCTAGGAGGACTAGCTGTGACCACTCACTTGGCTTAGGTTCTGGTGAAGACTATTCCTTTTGCCTTTTTCAAAACTCCCTTTCTGCTGCTGAGGGCCTTTGCTTCTTTTTGGGAAATACCACTTGATAAGGGGGCGGGAGATTTGGGTTCTGAGAAGGGGCAATTAAGCCGCCATCTCTGGGGTGAAAAAAAAACTCCCCTTCTTTTCTTTTCTTTTTTTTTTTTTTAAGAAGAAGAAGGTCCTGGCTGCTCAGCTACTTGGTGGCCCCCATCCTGGCAAGCCGATGAGGGAACTCATTGCTGTAGCGAGCAGCAATACTTAGAAATGCACCGAGCCTACCTGCACCATCTCTGAAAGCCAGGCTTG
Seq A exon
GTGAGTTCCTGGTGGCTGTGCTGAAGAGATCAGGTCTGGCAGCTGCCTGAATGTCTGCTCTGGGTAGGACCCGAGGTTGTAACGTTGTCTATATATACCCTGTAGAACCGAATTTGTGTGGTACCCACATAGTCACAGATTCGATTCTAGGGGAATATATGGTCGATGCAAAAACTTCATATATCTCCGACATGGCCAGAGACTGAGGCGCGGAGAGTACTGGCAGCCCAGCCGGCAAGCCACCTCTTTCTTTTTCATTACCTTAGACTCCAGGATGATCGACTTTGCCTGGTGAAATTGTACAGCCTTTTCCTGGAGAAACTCCTATAGATATTCCAGTAGGTGCTCAAGTGGTTGTCTGAGTGTAAAGCCAGAGAGCCAGGTTTTAGGGTATTAGAGAGTGAGGTGAAAGGCCAGAAAGCTCCAGCAGAAGCCCTGCTCTGAAGGAGCATGAGACACAAAGGTACCCAAATGGGGCTCACCTGCCCTTGTGTGGGAAGAAGACAAACTGAAAGATAGGCCATCGGAGACCGTTGGGGTACATTTAGGCAAGGTTAAGGTCCCCCTCCCCACCATCCCAATATGACCCAACCCCTCAGCCACCAGACTCAGAACTGTGAGGGCCTCCTGCAGAAAGATCCAACTTCAACTAGAAACACCCCAGCCTGCGCATTGGCAGAAAAGCATAGTGGTTACTCATTGCCTAACTCAATTCAGGTCCGCCAGATTCTGGTAACTTTTGGGTGACCCTGATGAAGACAAAGCCAAGACAGGTCTTTGTATGTCAGAGTCCAGGACTCCTGCCAGCTGGCCGGGCAGCCTGCCTGCCTGCCTAGGACTCTACCCAACTCGGAGGCCACATTGCCCACACTCATTCTTCCTTATTTTGCACCCCAG
Seq C2 exon
TAGGAGAATTCACTCTTCTTTGAACTATGTCCATTCTGGGGGCTGCTTCAGGCGATGGTGAGTAAGGAGGGCATGGGAGGTTAGCAAAGTCAGTGGAAGACAAAAGCCGAGATTACCTGCCGGAAATTGGGACCCCGGGGATAGAATTAGAACTCTATTAGCATCTGTCAGGGACTCTCAAATGTGGCATGGCAAGTCACTTGATTACACGTATGTTATTTAGTTAAATTTGTGAAAATTATGAGATGCTCACCAACCCGGTGATAAACATGCTTTCTTCCTATTGGCTGGCCTGGTCACATGGCCGCCCAACTTTATTCAGTTGACAGCAAGTAGGAGGGCCCAATGGAAGGAGAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCTAAGTACGTGGACCCCAAGTTTCCTCCGTGCGAGGAATATTTGCAGGGTGGCTACCTAGGCGAGCAGGGAGCCGACTACTACGGCAGCGGTGCACAGGGCGCCGACTTCCAGCCCTCGGGGCTCTACCCACGGCCCGACTTCGGCGAGCAACCCTTCGGAGGCGGCGGGCCCGGGCCTGGCTCAGCGCTGCCCGCGAGGGGTCACGGACAGGAGCCGAGCGGCCCGGGAAGTCATTACGGTGCCCCGGGAGAGCGGTGCCCAGCGCCCCCGCCTGCGCCCCTGCCTGGCGCTCGGGCCTGCAGCCAGCCCACCGGCCCCAAGCAGCCGCCCCCCGGGACAGCACTCAAGCAGCCCGCTGTGGTCTACCCTTGGATGAAGAAGGTGCACGTGAATTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042464-Hoxd4:NM_010469:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.727
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGGAGATTTGGGTTCTGAG
R:
CGGCAGGTAATCTCGGCTTTT
Band lengths:
356-1253
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: