MmuINT0033997 @ mm9
Intron Retention
Gene
ENSMUSG00000031326 | Cdx4
Description
caudal type homeobox 4 [Source:MGI Symbol;Acc:MGI:88362]
Coordinates
chrX:100516737-100523493:+
Coord C1 exon
chrX:100516737-100517394
Coord A exon
chrX:100517395-100523347
Coord C2 exon
chrX:100523348-100523493
Length
5953 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
ATCTTATGCTTTCTCAACAGGGA
3' ss Score
10.65
Exon sequences
Seq C1 exon
GGGTAGGAAAGGAAGGATGGAGTAGTCCGAGCCGCGCAGAGGAGCTAGCAGCGCTACTAGTGCTGACCGTTGATAGTCTCTTGCGTCTCAAACTCGGGTTGGCGCTAAGTTTACAGGGACCTCAGGATGGCTTAAGGGGCAACTTCTTCTATCCAAGTCACCATGTATGGAAGCTGCCTTTTAGAAAAAGAAGCGGGCATGTACCCAGGCACTCTCAGGAGCCCTGGAGGAAGCAGTACAGCCGGAGTGGGCACCTCTGGGGGCAGTGGTAGTCCTCTGCCTGCCTCCAACTTTACTGCAGCCCCAGTTTACCCACACTACGTGGGTTACCCTCATATGTCCAACATGGATCCTCACGGGCCTTCGCTGGGAGCCTGGAGCTCACCCTACAGTCCGCCCCGGGAAGACTGGAGTACATACCCTGGGCCGCCCAGTACAATGGGCACAGTGCCCATGAATGACATGACCTCCCCAGTTTTCGGATCCCCAGACTACAGCACTCTGGGCCCCACCAGCGGTGCAAGCAACGGCGGTAGCTTGCCAGACGCGGCCAGCGAGTCACTGGTTTCTCTTGACTCCGGCACCTCAGGCGCCACTTCTCCCAGCAGGAGCCGTCACAGCCCCTACGCATGGATGCGCAAAACTGTGCAGGTGACGG
Seq A exon
GTGAGTAATCCATCGTTCCGCTGTTTCTTCTCTTCTCTACCCTTGGTCCGCTACCCTCTTACTCTTCACTCTACGTCCCCGTAGGAGAGTTCAACTAAGCAGCCCACAGCGTAGCTGGCTGATGGGATCAGTAGTTCCCTCCTTTGCGCCTAGGTTCAAAGCCGGTTAAAAGTAGCGCTTGGAACTAAACCTCTCCTGGGGGTTGTTGAGGTGGGTTTGTTTGTTTGTTTGTTTGTTTAGGTGGTTGGTTGGTTGGGTTTTGGTTTGGTTTGGCTTTACCCTTTCCAGATAAGTCAAGGGAGTAAGGGTATGGACAGTGTTCCTGATGAACCACAAGGATCGGGATCCAATCCTGTCGTTGTCCGGAGGGAAAAAACCAGAAGCACATCATGATGAACAGGGTGAAGGACAGCTAAGGTTGTCATGGTGCTTGCCGGTTTTATCTCCAAATCTTTCCCTACCGCGGTATGCAGCCTCGCTGAAAACTTGTGATGCTCAACTTAGTAGGTGCTTAGCTGGCAACCGACGGCCGAGCCTAAGAAGGCTTCCAAGGCAAAAAACGGCCCTCGATACAAGATGCCTAAGGAAGCTACATCTTCCGTCGCCCAAATTAGAAATGTCTTGAAGCCTATTCCAATGTCCCTACCAACCGAAGGAAGCGTTAAGGTGAACAAGGTTACAGAACTGAGCTGTCATTTCATAGGACACAATCCTTACATCCGCCAGGCACACAACCCAACTGTTCCAAGTATTATTATCTCCCCCCCCCCACCCCCGCCACTAAGTGCCTAAAGCTCTCATAGCTATTTCAGCAGGTGGCCACAAATGCAGAAGCAGAATGCAAGTCTGCGACAGCGTCAAAACACTAAAAGGTGTAAGGACCCCAGTTTAAGGTCTAATGTCGCTGACCAATAAGCCCTGGCGGGCAACTGGGAGCAGCTAGCTGGTGGGGAGGGAGGCGCGAGCTTAGAGGAAATGAAGACTCCACTGTAATTCTTAGACTGGGAGCCAGTGACATGTTTGTTTACAGCTGTGGTTGTTCTCTTAACATTTTCTTATTATTCCAATACTTGTTCCCTGTCATTAGAGGACATTAGTGACATTTGTCTATCACATTCACCCCTCTGGGGAGGCAATGATATTTCAATAGTATTTGTCCATGTGTTTTCCCTTCTCGCTCTTCCAAAAAGCAAAGGTGAAAGGATAGGGAGGTAACATTTTTTTACCTTTAGGAGAATTTTCAGCCAGAAGGAGGAAGCTCCAGTTTTATAACTAGGGTAGAGATCCCAAGTTAAAAGTAACACTTAAGAACTTATATTAAGAAGAAAATATGGATAAGTCATGTAACTTTAAAAAATAATAATAAGGCTAGGGTAGGGCATTCATCCCCAGAACTGTTGTTACATCTAATCTTCAGGGTAAAAATAACATCCATTCACTAAAACCTAAGAATAAGCAAAATACATATTTTAAAAAGGACATAAAAATACCTACTGTCTAGGATTGTCCTTTGAAATACTGTAGGGGGAAATGTCACTAGCACATTTTTTAGAATGGAAAACAATGTGAGGAAAATGACACAATAAGAAAATTCAGTTGTGACGATTTGTCTTTGTGTTGCTGAGGGGAAACATGACAGTTTTCTCTGTTTTGCTTTAAGTCTTCCATATATATCTCAGAGCCTTCTTTGGGTAATTCTGATGCCAAGAGAAGTTGAGAAGGGATCCCCCCATCTACTCTGTGTTACTTCCTCTCTTCCATGTTTAGTAGAAGCTCAAAACTGAGAATGAGGTTATAGCTCCTTGGACTCTTGGCAACTTGTCCTATAGGCAAAGTTTTGTTAACATCAACATTTGTTTCATTTGAATTCCTTGTAAGTTAATACCATCCTTTTGCATATTCTTATAGTTCAGGTTGTTATTCATCAACAGTTTAAGATGAGAGCACCCCACACATATAAGTGATACTTTTCATAAGTTCTGGAAATTCTAGACTCACTGAATATCTTTCATGATATTGGGCCTTAAACTCCACAAAAATCAATGTCATCACCCCATTGAACACTCCAAACCAAAGTATACCCCTTTATATTAGCAAGGGAGCAGATGTTAAAGGTCTGTTAAGTGAACGGACAAGTCAGAGCTTCCTAAGCTTTCTCCTCACCTCCTACCATTGCACATGGACATAGCGTTTAGGGCTGAGAGAGAGAGAGAGAGAGAAAAATCTGTGGACAACAGACTGGATTAAAGCAATAACCCTTCCCTGAATTAAAGCAATCCCATTAAAGCTTTGTTTCTCTTTTTTTCATTAATGAAGATAATTGAAACAGACTTAAGTTAAAGTGTGTGTGTGAGTGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGCACTCATTACAGCTGTGATTTCTCTCTTTTTTTCGCTTTTTTTTATTAGATATTTTCTTTATTTACATTTCAAGTGCTATCCCAAAAGTTCCCTATACCCTCCCTGAGCCCTGCTCCCCTACCCACCCACTCCCACTTCTTGGCCCTGGCGTTCCCCTGTACTGAGGCATATATAAAGTTTGCATGTCCAATGGGCTTCTCTTCCCAGTGATGGCCGATTAGGTCATCTTCTGCTACACATGCAGCTAGAGACATGAGCTCTGGGGGTACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTCAGCTCCTCAGGTGTGATTTCTAAAGCATGGAGATAGACATGTAGAATAAACCTATTCTAAGCACATGCCACTATACGCAATCTATCTTATCCAAACATTTCTACAAATGTTAATATTTTCAAGCAGTCTCACATTTTAAACAATGCCAGTGTACGAGAACAAGTCGTTTTCCACTGTTTTCTTTAGTACAGAACTAAAGCCCTATATGAGTATTGGCCAAGCTGCATGCTTAGCACAGCTGGAAAGAGGCTTCCCTGTTTACAAAAGGAAAGGAAGTCATTTGAGCAATTCTATTTAAACCACTGGCCACTAAGGAAATACTTTAAAAGTTGTATTCAGTTAGGATACTTCATAAACTGAACTGCTTAATAATCCTTGAGGCCTTGGTCATTGTCTTCCTTGGTTTTTCATATTTTGTTAGACAACTTTAAAAGTGAGTTTGGATGTGATTTTTAGTTAAAAAGCAGTAAAGGATTGCCATTAGGTGAAAAGTCATCACGGTGGTACTGTCTCCATCGTTGTTTTGTTTTGTTTTGTTTTGTTTTCTTTTGTTTTGTTTTGTTTCTGTTCTCATCACCATTGTGGTCCTGAGGCTTCATATGGGCTTTTCTGCCTAATATTTCTTTGGCTGCTAGTCTCTCCACAGAACACCATTTCAACCACATTTATGGTGACAGTGTCATCCTATATAGTGACATCTCCTTGTGAACTGTGAGGTACTGCCTCCTGGGTGGTAGGAAGGACCATTGTGAACTATGGAGGTGATTGTTCAAGTCTTTGTGGAAGAAGTAACAAAATTCTCATTTCAGAGGAGTGGAAGTAGCTCTTTAATAAATCTTAGACTTTCTTCCATTCCTAAACTAACTCATAGTATCGGCTGAGAAGGAAATCCCCTGATCTCAAAATGTCATTGTCTCTAGAAAATAGAGGAACTTAAACAATAAAAACAAGTCCTCCTCATGCTTTGTTGGTCTTTGGTTTTAGTGTGGGAATATGGACATTGTGTTCTACCGGAAAGTGGCCAGATCCCTTCACTCATCTCAGGGGAAAAGGCTATTGGGGAAAGAGCCATGGTTCTGAGAATTTCTTTCCCTTTGTAAACTGTGCAGGTAGTTAGTATACTCCCTTGTCTTTGGGGTTTTCCGTCTTATCATCAGATTGGGCCTACAGACCCTTTTTAACACTTGTTCAGCTTTGATATGCATCTCAGCTCTTGTCATTACCCCTTTCTTCGAAGGTTATATTGCCGGAAAGGGTGAGCATTTTCATGGCAAATAAAGAGGCCTGGTCTTGACTTTATTGTCCTCAGAAGAAACTACAAGAGGGAAATTTATGACCAATGGGGGTTGGGAAGGACCACAATCTTTCCAGAGTTCTTGAAGTCTGGTTATATTTACTGATTAATTGGCTGAACTGAAGACACAGACACACACAAGTTGAATTTTAACCTTCCTCTTTCAAGTTAAAATTTAAACTCAGTCCCTTTTTTTTGATCAGGAAGGGTTTTAGGAACTATCTCCTCAAAGATATACTTTGATTCTAAAACCGAGGTCCTGAAAACCAATTAAACCTCAGATTTTTGTTTTCATCCTTCAGTATACATGCTGTCTTTGAAAGATGCCAAAAGCCAGATCCCTGGTTTCCTGTGTTTCTGCATGGATCCAGAAATCTGGATCGAAGTTTGGGCCTTTGAGGAAAGTTAATTGGCTGGGACTTGGGGCTCATCATTTCAAGGGAAAGAATTTTAGTTGCACTGAGTAGCCCATAAGTTATCTAGCCATTCAGTTGAATCCTAAGGTAGATCTGTTTCTACATCCAAGCCCCCTCCTCTTCCTGAAGATGAAAGGGTGTCTGACATTTGTTTAGGGCTTGTAAATTCCAAGCCAATTGGTTGATGTTCCTGAATGTAAAGAGGGTTCAGGATGGGATCCATGCTATGTGGCTCCTTTGTTAGGCCTGTGCTGCATCTTAACACCTCAATGGAGTTTAGGGACCCACTTTAAAGAGGTCTTTGTCCTACAGGTGGGGGGGTGAGCGCAAAACCTCACATCAAAAACAACCAGAGAAGATCAGAAGAACTTTCTAAAAGCCACAGGGGAAAAAAAGCGAGATCCTAGAGTGGGTTAGAGAAACTGAAAAGAAAGGGGGACTTCCTAATCACCTTTGCAAAGTTTGAAAGGAAGACTAAAACTCTATTTAAAGGCAAGCATGAGAAATTAGCTAGATGTTGTCACACAAACCAAATGTTTGGATATCTTTTCAAAGCACGTGGAGTCCTCACTTCAGTCTGCTTAAGTCAACACACCCTCCTCCCCCATTCACTGTTCACGTGGAAATAAAAAAAGCCTTAATATTCCCACAGGAAAAATAGTACTTTTTCTAATAAACATTAGGTGCCATTTTGAAACATAATTTGCTAAGTAGCAATTAAATATTTTCTTTTCAAACTATACAAAGTCTTTCTAGGTAATACACAGAACTACAATGTCAGGATTCCAGAATAGTTTGCTTCATGTGGGATTATACTTCCCAACAGCATACTAAGCCTAGAGTCAAAGGTCCATGCTTGGGTTTGCCCTCCTAGGCTCACCAGCACAAATTCACTTACCTATACTGAACCTCAGGTTCTTTGTCTATACAATAACATTCTCCATGTTATTTAACAGAGTAGATAAGATAATGGGAAACAGTCATGAAAGCATTGCAGAAAATGTAATTCATGAAGGCCAGCTATGGTGGTGCACACTTTTAGTCCTAGCACTCAGGAGGCAGAGAAGGGTATATCTCTATGAGTTTGAGGCCAGCCTGGTCTACAGAGCAAATTCCAGGACAGCCAGGGCTACACAGAGAAACCCTACCTCAAAACAACAACAACAACAATAAAGCAAAGTATAATTCATGGTGGCTGTTGCCATTATTGTTAATTCAATTATTATATTTGGATGAAAACTGTGTGGTTGAGTATTTAAATATTTTAAATGTTTTTGTATAACAGTAGGTAGAGTAGCTGTAATTCCACTGATTATTTCAGGACAATTATGGATGTTTATATTCACACCCAGGTAGGTATTGATAACATGATATGATATATTTGACATGATATATTTAGCTTAAAAATACAATTCCTTTCTATTTCAAAGTAATAAATGAAAGTTAGAAGAGTAACTGGTGCCCTCAACCCAAATAATCTCCAGAAGAGAAGAATAAGATGAAATCTTATGCTTTCTCAACAG
Seq C2 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTGGTCTACACAGATCATCAACGGCTGGAGCTGGAAAAGGAATTTCACTGCAATAGATACATCACCATCAGGAGGAAGTCAGAGCTGGCAGTTAACCTGGGCCTTTCTGAGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031326-Cdx4:NM_007674:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.807 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PU(97.5=92.2)
A:
NA
C2:
PF047317=Caudal_act=PD(1.9=6.1),PF0004624=Homeobox=PU(73.7=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]
Other AS DBs: