MmuINT0033994 @ mm9
Intron Retention
Gene
ENSMUSG00000024619 | Cdx1
Description
caudal type homeobox 1 [Source:MGI Symbol;Acc:MGI:88360]
Coordinates
chr18:61178516-61180173:-
Coord C1 exon
chr18:61180028-61180173
Coord A exon
chr18:61179596-61180027
Coord C2 exon
chr18:61178516-61179595
Length
432 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AATTCTCTGCAACCCCACAGGTA
3' ss Score
7.16
Exon sequences
Seq C1 exon
GTAAGACCCGAACCAAGGACAAGTACCGTGTGGTCTACACAGACCACCAACGCCTAGAGCTGGAAAAGGAGTTTCACTACAGCCGGTACATCACTATCCGGCGCAAGTCCGAGCTGGCTGCTAACCTGGGGCTCACAGAGCGGCAG
Seq A exon
GTATGTGGGTCCCCCACCTCAGCTCAAGTAGCAAGGCCCAGAGTCGGTCTTTCAGGCTGCCATGCATGGACAGAGCCCACAAAAAGAAAATAGAGAGGTTGTCTCCAGACTACTGGCACAAAACCACACACTGGACCACTCCCACACCCTCAACTAAACCCAACATTACTACATACACACAAACATATACACACACACACACACACACACATACCACGGGCTACAGTGGCTGGTAATCAATGCTATTCAGACCCAAAGGAAGGGCAGTCACAGAACACAGGAGCTCTGGAGAACTGGGGCCTTGGAAGGGGAGGAAAGAGGTTTCAGAGAAGGGTGTCTGGTGTCAGGAGCAGAGAGTGGATCATGAAGACCCCCTTCCCCAGCCCAGCTCTTTCCTAGCACCTGCGGTATAAATTCTCTGCAACCCCACAG
Seq C2 exon
GTAAAGATCTGGTTCCAGAACCGCCGGGCCAAGGAGCGCAAAGTAAACAAGAAGAAACAGCAGCAGCAGCAGCCCCTGCCTCCCACACAGCTGCCCCTGCCCCTGGATGGCACTCCCACACCATCAGGGCCACCCCTAGGAAGTCTATGCCCTACTAATGCTGGCCTTCTGGGCACCCCCTCCCCAGTGCCCGTCAAGGAGGAGTTTCTACCCTAGCCCCTTGCAGCCTGGGGTCTAGGGATCTAGGGACTTGAATGCTGGGCAGCTGGCTTTTCTGGGGCCCAAGGACCTGTTCTGAGTTGCAGCCCTGCTGCTGCCCTTTGGGGTCACTGTGGACAAACTGCCTACCTAGGACAAGTAGCTTGCCCTCTTCCTGCCTTCCGTTGGCTGGGCTGTGTGGTGAGCCTGTTGGACAAGGACCTCTTCCAGCTCTTGTGTCCTAGGCCACAGGGTGATGGGGAAGCCCAATGAGAAGTCTCAATCACCTGGAGATTTCCCAAGATTCAGAGGGCTCAACGAGCTGTCAAGACAAGATTGAGGCTTCACCGTCTCCTCCAAGGGTTCCAGAGTGAGGTGGGAGGCTGGTATCTGGACCAGACTGGCTCTGGAGAGTAGGCGGCATTGAAAGAAGGTGGTACACCAGAGTCTAGACTCCCATGTGAAGCACAAGGATGCTATCTGCCCCACCTGTCTCCTCTTCCAGCCTCACTTTCACCTGCCCTAGCACCCCATGCTCTGGCCCTCCCCAGCCTGGAGCTACAAAGCCATCAGGACTGGACATGAGGTAGAGGCTGGGCAATTGGCCACTGCTCTTGAGACAGAACTCGCCCCCTCCTTAGTGTCCAGGGAGGCCTGCGGATGGAGAGGAAGGCTCTATGAGTCTACCTACCTGCTCATGCCCACCTTCCCACAGGCTGCCCATCACACCCAGGGAGCCCCCAGACCATGGGGGACTCGCAGCTGTACAGGGCTTATGTAGAGTGGAATCTCTTGGATGCAGCTTCAGAAATAAGTTTTCCCCCTTTTAAACAATTTATAAAAATCATACATGGCATTAAAGGAATTTTTTAAAAAGTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024619-Cdx1:NM_009880:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.901
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.1)
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:
TACACAGACCACCAACGCCTA
R:
TAGATCCCTAGACCCCAGGCT
Band lengths:
356-788
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: