HsaINT0032889 @ hg19
Intron Retention
Gene
ENSG00000131264 | CDX4
Description
caudal type homeobox 4 [Source:HGNC Symbol;Acc:1808]
Coordinates
chrX:72667090-72673498:+
Coord C1 exon
chrX:72667090-72667591
Coord A exon
chrX:72667592-72673352
Coord C2 exon
chrX:72673353-72673498
Length
5761 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
AATGCTTTCTCTCCTAACAGGGA
3' ss Score
11.68
Exon sequences
Seq C1 exon
ATGTACGGAAGCTGTCTTTTGGAGAAAGAAGCAGGCATGTACCCGGGCACTCTCATGAGCCCTGGGGGCGACGGCACAGCTGGGACAGGCGGCACAGGGGGCGGTGGGAGTCCGATGCCAGCCTCCAATTTCGCTGCGGCACCGGCTTTCTCGCACTATATGGGGTATCCTCATATGCCCAGCATGGATCCTCACTGGCCGTCTCTGGGAGTCTGGGGCTCACCCTACAGTCCCCCGCGAGAAGACTGGAGCGTGTATCCTGGGCCGTCTAGTACAATGGGCACAGTGCCGGTGAACGACGTGACCTCTAGCCCCGCCGCTTTCTGCTCGACCGACTACAGCAACTTGGGCCCTGTGGGCGGTGGAACTAGCGGCAGCAGCCTACCAGGCCAGGCTGGCGGGTCGCTTGTCCCGACGGACGCAGGCGCCGCCAAGGCCAGTTCCCCCAGCAGGAGCCGCCACAGCCCCTATGCATGGATGCGCAAGACGGTGCAGGTGACGG
Seq A exon
GTGAGTAATCAATTCCAATGCCCACACACTTTTCCTTCCTTCCCTTCTCCGCTACTTCTCTTGGTCGGCCTGCCCTCGTACTTCTCAGGCCTCTCCCAAGAGGGCTTAGCTGAGGCGACCCCTATATGGCTGGCTGGCCTATTAGGCATCTCCCTCGCATTCGCCTGGGCTCAAAACTCACTCACTGAGTGCAGCGATTGGGACTAAACCTACCCTAGAGGTGATTTTCGCCTTTCGCTGCTCCATGAAGAAAGCGAGTGAGTGGACAATGGGTATGTTAAGCCACAAGGATCAGGATGCAACCCTGTAGTTGCCCACATGGGAAAAGAGATGCATGAGAAAGCTCAACGGGTGAATGAAGCGAGAGGGCAGCTGTAGTGTCCCGTTGTTCAGGCACTGCTGCTTGACTGTTCCATTTCCAAACCCTTACCCATCTGAGCGGGCTGTCTCCCCCCTCCCCGCCCCCAAAGCTGGTGATGCTCAATTTAGGTTCACAGTGCTTGGCTGGCAACGGACCCTCCAGTTTAGCCACTAAGTCCCCGACGGCAAAGCAACCTCTTCACCCTGGCCTCTCAGGGAAGCTCCAGCTTCCTTCCTACAAGTTGGCAGAGGCAAATTGGCCTAAAATCCATTGCCATCTTACAACGTCCTTTCTTCTAACCCAAGTGTTGAGGCAGGCGAGAAGGCTACAGCACTGACCTGGTACATAATACGGTACCTAACCCTCACACCCGCCCGACACGCAAACGAATCAGCTCCAGCACTAATAAATGGCTAAAGCCCTCATAACTATCAAAGCAGGCGTCTCTCAGGCGTGGGGGCTGAATGCAGGTCTGCGGCAGCGCGAGAGAAGTCAAAGCGATCGCGATCACAGCCTAACCAGCAAGCCAGTGGGCGACTGCTGGGAGCCAGGGCGAGGGAAGTGGCCGTTCCACTTTAATCTTAACCGGGGCTGGGGGAGGAATGTTTGTTTTCAACTGTTGTTCTTTTATTACATTCTTATTATTCCAACCCTCGCTCCCTGTCATTAGAGAAAATTAGTAAAAATCGACTCTGAGTATTTTCATCCCTCTGGGGAGGAAATGGCATTTCAATAGCATTTGTCCGCAATGATTATGCTCCTGTTCTCAGTTCTGCACTTTGTCTTTCCTCCAAAAAGCAAAGACAGGAGGGTGGGAAGTGACCCATTTTTACCATTAGGAGAACTTTTAGCCAGGAAGAGGAAGTTCTGTGTATTAGAACCTCACTAGAGTAGCGATCCCAAGGTAAAAGTAGAGTTGAAATACTTGGCTTTAAAGCGTTTGCAAGTAAATCTGCATTTTAAAAAAATATGAGTGAGTCTGTCGACTAAGTAGAATAGAAAAAGAGGTTAGGGTGGGGCACTCCCAGAGTTTTTATTACATCTAATCTCGGGGTTGTAATTAACATCCACTCACTAAACCCTAACAATCAGCAAAAGACACAAAAGCTAGAAAAGTAGTTGCTCGCAGTCTAGGATTATGTTTTGAAACACATTAAGAGGAAAGTCACTGGCGTGCTGTTTGCAATAGAGAACAAGAGAGGAAATGGATGAGATAAAAGAAATTATCTCCAGCCTTGAATTTTCTATTTATGAGGAAAAATATGACAGTTTTATCTGCTTAAAGGTCTTCCGTTTACATTTGCTTTTATTAGCCTGAGTCTCTCTCTTGGGCAATTCTAATGCCAGGAAAGGTTTCGAAACGGGCTCCTTAGTCTCTTGCATCTTTGAGCTAAACCCTCAAACCTGACTTTACAATGGCACCGTCACAAGATTTTCTATCCAATTTCTATGAGAAGTTTAAAATGGAATGATATTGGAACCATTTCGATTTTTGGCAGCCTATTCTATAGATGAGGCTTCATTAAATTAAAACTTCGTTTCATTTTAATGTCTTATAAATGAAAATAACCCTTTTGCTGTATTCTTATAGTCTAAGGTGCATATTTAGCAGCAATTTAAGAATATGATGAAAAACTTTGGTTATCTCCCTAGAAAAAATGCACAAAGGCACAGCAGCACACACACAAACACAAGTAATTTGTTACATAATTTTAGGAGATTCATGGATCCATTGAAGCCCTTTCAAGGGACATCAGGTTATAAACCCCACGAAAAAAATTAAGCTGATCACCTCACTAGGCCACCCACTCAGGACCAAAATGCACCCATTTATATGCTTAGTACATAGTGGGTCTTAAATATTTGTTTAATGAATGAATGAGTCAGATCCTCCTAAATTTTCCACTTCACTCTGTAGTACTGTGGGATAACATATGGTTTATGACTGAGAGGAAAAGATGAACTTCAATATGGAAGTAACCCTTGATTAAGGTAGTCAGATGAAAGTTCTTTCCATTACTGAAAAATGTCTTAAATAAATGTAAAAAAGGAAAAAATGCATGTATTAGTGGACAATCAGAAAACATTTCATAGCGACCATTATAGCATGTTATTTTCTAATGAGAGCAAGGAGGCTGACAGATAGAGTAAATGACTGTTCCCTAAGTGACCTGATTTAAAAAGAAGGCATGTTTATTTCCACTTAGTTCTCTAAGTGGTCTATTTCTATACATATCTAACTTTAAATATTATGCAAAAAGGAATATGACAGAAAAGTTTCTATGGAAAATTTAATATTTTCATGCACTTTCACATTTTAAACATTGGCAAGGTGATAACCTAAGCAGGCTGGAGAGAGGCTTTTCTGTTAGAAGTGGAAAAGAGGGGGAGAGCAGGAAGTAATTGTGATTGATTCTGATTCTGATTGATTGTTTTAAGCCACTGGACAACATGAAGGAATTTATGCTTGAAAGGCATTATTCAATAAGGACACTTCATAAAATTAGTTGCTTAATAATTCTTGAGAGTTATCATTGTCCCTTGGTTTTGCTCATTTCATGGGACAACTTTTTAAAAATGAATTTGGATGCAATTTTTAGCTAAAAACAGTGAAATATTACCATAAGATGAAAAGTCCTCACAGTGGAGTCCATTAGACAGTACTCCCTACATAAGAATATTCATTTTCATAATCTTTACATTCACTCCCATCATCATCACCTCTATGTTTGGAGAGTGACTTTCTGCCTAGCAGCACTTTTGCAGCCAGTCTTTCAAATGAACACCATTTTAATTTTATTTAGGGTGATAAGTTATCATATATTATGACATTTGCTTGTGAATTCTGGGGAGATAATGTGGTTGGGAGGATGGGAAGGACTCCATCCATCTTTAACTACAGAAGTTTTTCTGACTCTTTGAGGAGAAGGCAAATACATCATAGATAGTATTAATTTCCTAAATAAACTCAATAATGGCTGAAAATGGAGCCCATCACCCTCAGAAATGTCATAGTCTCTGGAAGAAGAGAACAGCTTGAACAATAAAAGTTAGTTCTGTTAGTGCTATTTTTTTGGTGCTTGGGTATGGGAATATGGACATTATGCTTTACCAGAAAATGTCCAAATCCCCTTCATCATCTGTTCTGGTTTCATCATTTTATCTGGTTTCATCATTTAAGAAGAAGGGGCAATGGGATTGAGAGAGACAATTTGAGGAGCGGGACACAAAAGGAGCACCAGGAAATTCAAATTTATTTCTCTTTGTAAACTGTGCAGTCAGTTTTTTCCCCTGAGCTACATCTTCTTGGAGTTTTAGGTCTTATCTGTCAGATTTTGGCAACAGACTCTTTTTAACACTTCACATGGCTTTGATATGCAGCCAGGATCTTCCTTATCCCTCCTTTCTTCAGGGGTTATATTGCCGGAAAGGGTAGGATTTTTATGGCAAATAAAGGGGCCTGGTCTTGACTTTATTGTCCTCAGAAGAAACTGCAAGAGGGGAATTTATGACCAATGGGGGTGGGGAAGGACTACAACATTTCCAGAGTTATTGATGTCTGATTATGTTTATTGATTATCAAAGAGCATAAAACATGGATAAAGACAAGTTGAATTTTTAACCAGTCTGCCTCAAGTTATAATTTAAACACTCAGCAACTTTAAGATTAAGAAGGGTTTTAGAAAACATGATTTCAAAGATACATTTCGATCTCAAGATTTGATGTTCTAGAAATAAATTAAATCTCCAAGTTTTCATTTTTTTCTCTAAATATGCATTCTGTCTTTGCAACATGCCAAAAGGCAGACTTACGGTTTCCAGGTTTTTGCTTAGACTCAGAAAACCAGCTCAAAATTTAGGATTTTAAGGTAGGTTAACTGACTGGACCGCATAGTTTTCCTTTTCTAAGAGCGGGAAAAGGAGATTTTGTTCAGTTCATTATTTAGCCATTTAGATTAATCTTAAAATATATCACTTATCTAAAATTTATTTCTTCACTGGTGTCCTTTTTTTTTTTTTTTTTTTTTCCTTTTCTGGAGATGAAAGGGTGTCTGACATTTGTTTAGGGCTTGTAAATTCTGAACCAATTGGCTGGTGTTCCTGAATGTAAAGAGGGTTCAGAATGGGATCTGATGCTATGTAACTCTTTTGTTAGGCCTGTGCTGTATCTTAACACCTCAGTGGAGTTTAGGGAACCACTTTAAAGACGTCTTTGTCCTACAGATCGCCCCCAAAAAATCACATAAAAAACAACCAGGGAAGATCAGAAGGAGTATTTAAAAGCCATAGAGAAAAGGAGGAAGATCCTGGAGGAGGGTAGAGAAATTAAAAAGAAAAGAGAACTTCCTAAGTATCTTTGGAAAATTTGAAAGGAGGAATAAAGCTCTATTCGAAGGAGGGCATGAGGAATTAGTTAAATGTTGTAACACAAAGCAAATGTTTGTATATCCTTTCAAAGGGCATGGAATACTCACTTTATTCTGCTTAAGTCAACACCTCCTCCTTCCCCCATTCACTACCTACTTGGTAATAAAAATTAAGACTCCCACATAAAAACTATTTTTTTTTCTAATAGGTAATGGGGTTTTCTGAAACAGAATCTGCTAAATGACAATTAATGTTTTCTTTTTAAATTACTATTCAAACCAAACTCTAGGAAATTATGTAACTATAATGTTAGGATCCCACAAGTGTTTTCCACTCTTGGGCCATTATTATGCGTCCCAGCATATTTGAACTTGGAATAACATTTAGTTAGCATACTTAAATAGGAGTCAAAGATATGTGTTTGGGTCCCCACTCCTCAATTCTCTAACACAAAGTCATTTACCTTAACTGAGCTTCATGTTTCTTATCTGTAAAATGGAGATAAGACATGTTCTGCATAATTCAAGAAGGTAGGTAAGAGGTTTAATAGGAACAGTATGAAAAGACTGCATAAAATGTAGTGGGAAGTGCCTGTATAATGGACAGCTGCTATTACTGCCAATGCTAATCACATATGTAAGTGGGAAGGTAATAAACACCATGGGTTAAAGTGTTTAAGCATTTTCAATGCTCTGCTGTGAAAATAGGTCAAGATGGGATGATTGTGATTTGACCAATCATTTTAGGAGAAACATTAATTAAAGAGATGTTGGTTTTATATATAAGGAGAGATATAGATATAGAGATATATGTCTATGTCTATAGATGGTAGACAGAGATATTGCTATCATAGCCACAGATGAGAATGTATTTAATGGAGAAATTGACTTTTATGAATATTTGATTCAAAAATATACTTATTTTATATTTTAAAGCAAAGATGAGGGTGGGAAGAGTGTCTATGATTTCTTTAACTAAAACAATCTCCAAGAAGCAGAAAAAGATTAAATGCAATGCTTTCTCTCCTAACAG
Seq C2 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTAGTTTACACTGATCATCAAAGATTGGAGCTGGAAAAGGAATTCCATTGCAATAGATATATCACCATCCAGAGAAAATCAGAGCTGGCAGTTAACCTGGGCCTTTCCGAGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131264-CDX4:NM_005193:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.601 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PU(97.5=92.3)
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
Other assemblies
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)