MmuINT0033995 @ mm10
Intron Retention
Gene
ENSMUSG00000029646 | Cdx2
Description
caudal type homeobox 2 [Source:MGI Symbol;Acc:MGI:88361]
Coordinates
chr5:147303181-147307270:-
Coord C1 exon
chr5:147306445-147307270
Coord A exon
chr5:147303327-147306444
Coord C2 exon
chr5:147303181-147303326
Length
3118 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AACTTCTCCTTCCTCCACAGTGA
3' ss Score
9.26
Exon sequences
Seq C1 exon
GTAAGGCCGCTGGCCTGGGACTCCGCGAGCCAACCTGCGGCGGGTCATCCCCGCCTCTACAGCTTACTGGCAAGGAGGTGGGAGGAAAGAAGGAAGAGAGGGGAGGAGGCAGGACGGAGGGAGGGACTGCCCGGGAGGCAGAAGCTCTGCAAGGAGCCGACGGAGCACCGTGGGCTGAGGTGCAGCCAGCTACCTTTATCTCTAGCCCCCTGCGCCTCGCGCCTCTGGCAGCCTTCAACGTTTGTCCCCAGACAGCATGGTGAGGTCTGCTCTGGGTCCCTCGCCACCATGTACGTGAGCTACCTTCTGGACAAGGACGTGAGCATGTATCCTAGCTCCGTGCGCCACTCCGGCGGCCTGAACCTGGCTCCGCAGAACTTTGTCAGTCCTCCGCAGTACCCGGACTACGGTGGTTACCACGTGGCGGCCGCGGCGGCTGCTACGGCGAACTTGGACAGCGCTCAGTCCCCAGGGCCATCCTGGCCCACCGCGTACGGCGCCCCTCTCCGCGAGGACTGGAATGGCTACGCACCCGGGGGCGCTGCGGCAGCCAACGCGGTAGCCCACGGTCTCAATGGTGGCTCCCCGGCCGCCGCTATGGGCTACAGCAGCCCCGCCGAATACCACGCGCACCATCACCCGCATCATCACCCGCACCATCCGGCCGCCTCGCCGTCCTGCGCCTCCGGCTTGCTGCAGACGCTCAACCTCGGCCCCCCGGGGCCCGCAGCCACCGCCGCCGCCGAACAGCTGTCCCCCAGCGGCCAGCGGCGAAACCTGTGCGAGTGGATGCGGAAGCCCGCGCAGCAGTCCCTAGGAAGCCAAG
Seq A exon
GTAAGCGGTGCCGGGGCGCGCCCCAGGTCCCGCGTGCGTTGGGGCTGTCGCGGGCTGTCTGCCAGCTCCTAGCCAGGACAGGAGAAGGGGCAAAGGGGGAAATACAGGTGGATTCATCCCAGGAGTGTATATTTGTGTCTCGCTCCCCCAGGTTTGTTTAGGGCAGTACCCCATTGGCAACCTCGGGACGCCTTCGGAAGCTCCCGGTAGTGTCCTAAGCACTGTCGCCCGCCGCGAGCTGAATCGTGCCCTTGAGTTGGCTGCCTCCCGCATTCCTTACACCGTTCCTGGCCGAGAGGGTCGGGCCGCTTGGATTCTCTTTGCCGTGCCTACTCAACTTAGCTACCTGCTTTTCTTCTTCCATCTGAGGTACCCCCCCGAAAGGGCCAGGGAGTGTGGAGGCTGCGCCAGGATCAGTTTGGCCATTAGGGTCTACTGAAGGGGTCGGTGCTGCTGCGAGCACAGACGCCGCGGTGCGCCCCTGGAGAGAAGGCGGAGCCCCCCAGAAGCCTCGGAGGAAGTGGGGGAACTCCAGGGTCCCTGACTCTTCCCTCTCTCTGCCAAGCAAAGTCTCTCATAGAAATCCTCTCTTAGCATCACAGCGGACTCGGCTTCTTAAGAAGGTTTCTTCCTGACCCTTCCCTTCTAGAATCTCGTGTGTCTGAGAGTGTTGTGTGTTGGATTCGGGAGATTTTTCACGAAAGACCCGAGATTGCCGGTCTGTGGGACTCACAAGCTCTGTTTGCCCTTTCTGATGTCCGGATGTGTATAGGAGTGGGAAGGAAGTGAGCAAAGTGTGACAGGGAGTGGTACTAAGAGTCCCCCCTTTTTTGTTGTTCCGTGAAGCCTTCTCCAGCTCTTTGAGCTTCCGCTTCTCTGGATTTGCTCCTTGTTGGCACAGCCAGGCCACATGCCCGGGTTATGGCCACTTTGAGGAGGTTTATAGCCAATTACAGCCGTATAAATCAGAGCGGCACTTGGGGGCCTGTCGCTGGACACTTCTGCGTCACTGCGCACACCCCGTCAACATCTTGGTGGGCAATGCTGCCGGAGTGAAGTCTCCAGATTAGCCTCCAGTGGGCTTTGACATTGTCATTTCCAGGAGGACTTACTCCTAAACCGGTTCTCCGCATAAACCCTACTTTCCCAAGCCTGCCTGAAAGGTAGTGAGCGGAGGATCGCCGGTAGGGGTCTTAGCCCTCCGAAAGAACTTTTGCGTTCAGGGGGTGGGTGGTCCGAGACTAGGGTCCTGGGAGGGGGAGGAGAACCTCAGGAGCCCAGGCCGCGGGGTCAGCAGATGAGAGGTCGCTGTGAAGTCCCGCGCCGAGGTGGCAAGACCGCTGTCGGCGCCGGGCGCCCTTGTGATGTTAATGTAGGGAAGCTGTGGCCCGCAGTGCCGGAGCCCGACTCTTCTGCAGAGCGTCATCTGTCAAGGGGCAGAGGCGTGTACGCCGCCCGGCCGGCTTTGATGTACACCTTTCAGCCCTGCCATTGTCTCTTTTAGGGCCCGGAAAGAGGGTGGTGACTTTCGCAGTCAATAATGAATTCTGACAACTCCTTCTCATCCCTCCCCTCTTCCAGCCCCCCTCCTTGGTTCCCAGGGGGTGCGGGGCGCCTGCAAGCCCTTGGGGAGCGGACCGCAGGGCTCACGGACCATCTTTGCGTTCCTCAGCCAGCGCGTGGTGCTCTAAGAGCAGCATCCGTTCTAGGGCGAGGACCGCTGTGGGAAATTGTTCTGCGCCTCGCTTCCCAGGTCTGATAGTTTTCTTTAGTACTACAAGCTCTTTGCTATTCGGTCTGCACACTTAAGATTTGGTTCTGTCGTCTTCTGTGGAGTGGGGCACTAGCGAGTGTGTTACAGGCTCCAGTGAGCCCGCTCCCGACCGGTTGGATCCCTTTACTTCCAAAGCAGGCGCGGGGTCGGGGCCGCAGCGCCCATTCAAATGCGCCTGCGGGGCTGTGTTTATGTTAATGCTCCTGGCGGGGAAGGGGATGAAAGCTGAGGCCGCCATTTGCTCAGTAGTGGTAATTCAAACAGAATGCGGTTGTTATTAAGGCATTGAAAGCGCTTTTCTTTGATAAGATCGCCTTGTCTTGCATTGTTTGCGACTGTGTTCCCCTTTCAGCGGCGGGGGGACCTCTCTCTGATCCCTCCTGTATCTTCCCAGGACACTTTTGTAGTGGTTTGCAAAGGTTTTTACCTGAACAAAGTCAGCCTGCGGGGCCTTAAACACCCCTGGGCAACTCCCACCCCTTAGATCTCCTTGTTCAACTAGGCACTGAGCACTAAAATCTATCTGTTTTGATGTGAGACCTCTCCAACTTTGGACGTGGAACAGTTCCTGGCCAGCATTCTGTCCATTGAAGCATCCCCGACTTAACCGGGTTGAATAGCCAGACTCCTGCCTGATCCAGCAGCCCCGCGCTATTTGTCAAGGTCCTTCAGTAAAACAATCAATCCAAGATTTAATATGTTGACTCAATCCAATGATCACAGGTCACTTGGTCAGGATAGTTGCCTCGGGGGATAAATGGGAAATTAAAAAAGAAAGAATGCCCCAGGCCAAACCTAGCTGGGCAGGTGAGACGCGTTCCAAGTAGAAGGATTTTCCTCCTGACAACATGGAGATAGCACTCAGAATTCCAGGGCAGGACTTTGTGTGTGGTACTGGTGACTGGTGGGGATCTGCCAGCCCATGCATCCATCTTTCCACTATATTGAAACAAAAGGTAACTACCCGCTTACCTTGACGCCACATCCCAGGTATTTTCAAAGTGGCCTGCTGTTTCATTTCTAACAAGTCTGAAAATGTGGATATTGATATTCCTGGGGACTCTGGTCACTTTCCCACCGCCCTTTTTTCTGATCCTAAATATACTATATTTGATTTATGGAAAGGAGGGGTGCTGTGTGAGAGGTGTTCCTTTCAGGTTAGTTGTGCCTCCAGGCTTACACCCCCCTTCCCCAGGATCCTGTGAGTGGATATTGTCAACCTGGGTAGTAGACACCCCCCTCCATCAGTGGATGGAGAGAAATGACTCCTGGGTTAGGGAGGTTTGTCATTACCAATGACTGATGGATTGTAGTTCTTAGCCAAAACTTCTCCTTCCTCCACAG
Seq C2 exon
TGAAAACCAGGACAAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTTTAGTCGATACATCACCATCAGGAGGAAAAGTGAGCTGGCTGCCACACTTGGGCTCTCCGAGAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029646:ENSMUST00000031650:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.589 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=WD(100=92.8)
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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