HsaINT0032887 @ hg19
Intron Retention
Gene
ENSG00000165556 | CDX2
Description
caudal type homeobox 2 [Source:HGNC Symbol;Acc:1806]
Coordinates
chr13:28539007-28543317:-
Coord C1 exon
chr13:28542603-28543317
Coord A exon
chr13:28539153-28542602
Coord C2 exon
chr13:28539007-28539152
Length
3450 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CACTTCTCCTTCCTCCACAGTGA
3' ss Score
9.78
Exon sequences
Seq C1 exon
GGGACCGCCTCGGAGGCAGAAGAGCCGCGAGGAGCCAGCGGAGCACCGCGGGCTGGGGCGCAGCCACCCGCCGCTCCTCGAGTCCCCTCGCCCCTTTCCCTTCGTGCCCCCCGGCAGCCTCCAGCGTCGGTCCCCAGGCAGCATGGTGAGGTCTGCTCCCGGACCCTCGCCACCATGTACGTGAGCTACCTCCTGGACAAGGACGTGAGCATGTACCCTAGCTCCGTGCGCCACTCTGGCGGCCTCAACCTGGCGCCGCAGAACTTCGTCAGCCCCCCGCAGTACCCGGACTACGGCGGTTACCACGTGGCGGCCGCAGCTGCAGCGGCAGCGAACTTGGACAGCGCGCAGTCCCCGGGGCCATCCTGGCCGGCAGCGTATGGCGCCCCACTCCGGGAGGACTGGAATGGCTACGCGCCCGGAGGCGCCGCGGCCGCCGCCAACGCCGTGGCTCACGGCCTCAACGGTGGCTCCCCGGCCGCAGCCATGGGCTACAGCAGCCCCGCAGACTACCATCCGCACCACCACCCGCATCACCACCCGCACCACCCGGCCGCCGCGCCTTCCTGCGCTTCTGGGCTGCTGCAAACGCTCAACCCCGGCCCTCCTGGGCCCGCCGCCACCGCTGCCGCCGAGCAGCTGTCTCCCGGCGGCCAGCGGCGGAACCTGTGCGAGTGGATGCGGAAGCCGGCGCAGCAGTCCCTCGGCAGCCAAG
Seq A exon
GTAAGCAGAGGCTGCGCCCCTTCGGAGGGTGCTTGGGAAGGCGCGGGTCGAGCCAGTGGCTGCTGCGCGTCGCGCGTCCAGTGCGCACAGGGGCGTCCCGGGCTGTCTGGGAGCTCGGCGCCAGGAGGGGCACGGCCCGGAGACAAATTCGGGGGCCTCTGGCCCGTCGGGGCTTCTCTGACCTACTGAGCCTGGGAGTGAATATTCTGAGTCTCAACACCGTGTTCAGGCGTCCTCTTTCCAAGAGCTCCTCATTCGCAACCCCGGGACACCTTCGGGAAGCTCCGGGGAATGTCGGCGTGAGCACTGCTGGACGCCGGCAGAATCGCGTCCTCCGGCACTTGCTGCGGCATGCATTCCTTGCGTGGCTCCTGGCCGCCGAGGAGAGAGGGAGGCTCGAACCTTCTTGGGCTAGGTCTAGGCCATTTATCTCCGCTCTCTCTTTCCCCATCTGAGCCATCTAAGAAGAGAAGTGACCTGGGGGGGTCGGAGGATGGCTAGGCTGTGTGTGGGACCGGGTTTGGCCACTCGGGCCAATTCAAGGTACAGCGAGCAGGCAGACCAGGGAGAGCTGCTGTCGCTGGGAAGAAGGTGCTAGCCCCAGCTGCTAAGGCGACGGGGGCGCGCCCCGTCTCTGAACCTCTGACCTGTGAAGGGGTCATTTCAAGCAAAAGCTGGAAGGCTAGGGGCAAGAAGCCTAGGGGCAGGCGTCTGCGGAGAGAGCAGGGAGACGGGGAGGAAACCCTGGTGGGAATTAAGCCGCCGCTCCAGGTAGGGGTCATTTCTCCCAAAGCTTCCTTTCAAGGGTGTCAGGGATGTCTGTGAGTGTGTGTGTGCAACTGAAAAAGATCCTAGGTTTGCCGGACTGTGGGGCTCATTGACTCTGGGTCTGCCCCTTCTGGTGTTCGAGTGTGCCTAGAGGTGGCAAGGAAGTGCGGTGGGGAGAGTCCTAGTTGAGTGCCCCTTTTAAAGTCTTTCCCCAGCCCTCAGCGCTTCCGCTTTTCTTGCTTCGCTCCTTGATGCCCCAATTGGGCAGGCACGCTGGTTATGGGCACTTTGCAGAAGTTTATAGCCAATTACAACTGTATAAATCAAAGCGCCCTTTGGGGGCTGTCTCTGGGCATCGGTTTCTGCGTCACTGTGCACATGCTAGGGAGAGTCCTGGTGGGAATGCCGCCGACCGGGGAGAAGGCCACAGATCAGCCTCGGGTGAGCCTCAGAGCTTTGGCTTGGTCCCTTCTCCTAGAGGAGGCGCCTTTCTCCTAGCAGGGGCTCCCAGATCCTGGCTCCCAAAGACCCACTTTCTACAGCCCCTGTCTGGGGCGCGGTTGGCGGGGGTGGCGCACGCCCTAAGGAAGACCTTTGCGTGTCCCGGGAGAGCGGCCGCGGGGTGAGGGCCGGGAAGGGGGCGGGAGGGAAGCCGCCAGAGCCCAGGCCGCGGGGTCAGCAGATGAGAGGCCGCTGTGAAGTCCTGCGCCGAGGTGGCAAGGCCGCAGTCGGCGCCGGGTGCCCTTGTGATGTTAATGTGGGGTGGCCGCAGCCCGCGGGCCGGAGCCGGGCTCCTCTGCGGAGCGTCATCTGTCAAGGTGTGGGGGTGGAGGGGGGGACGCGGCCTGGCTTGCTTTGATATACACCTTCCCAGCCCTGCCATTGTCTCTTTTAGGGCCCGGAAAGAGGGTGGTGACTTTCGCAGTCAATAATGAATTCTGACAAGTCCCTCTCATCCCTCCCCTCCATAGCCCCGCTCCTAGGTTCCCAGGGGGTGTGGGGCGCCTCCAAGGCCCTTGGGGCATGGGTCGAAGAGCGCTCAGGGTCTGGTCATCGCGTTGCCCGGCACGTCCGGGACACTGAAGGGGCAGCACCCGAGCAAGGGTCGCTCCGAGACACTTCCAGGCGAGTCTCCCTCCCGGGGTGTTCGGCTGAGGGAACTGCCCTGCGCCTCAGCTCCGGAGGTGTCCTCTGTGGCTCCAGCCAGGCTCCGGTGCCAACCCCGCCTGATACTATCTGCGTGACCCGGTCTGATTCTCCATTTCCTCATCTGTAAAAAGGGGCGAGTACCAATGGCAGCCTGGAGTGGGTTTGAGGCGGTCACGCGTGTCCGAGCGTCCACCGCGGAGAAAGTCGCGTTAGTTCCCTTTACTTTCATAGCAGGCGCGGGGTCGGGGCCGCAGCCCCATTCAAATGCGCCTGCAGGGTCGTGTTTATGTTAATGCGCCTGGCGGGGAGGGGGATGAAAGCCGGGGCCGCCATTTGCTCAGTAGTGGTAATTCAAACAGAATGTGGTTGTTATTAAGGCATTGAAAGGGCTTTTCTTTGATAAGATCGCCTTGTCCTGCATTGTTTGCGGCTGTGTTGGCCTTTCAGCGGCTCGGGGGAGCTCCCTCTGATCAGGCCTGTATCTTCCCAGGACGCTTTTGTTGTGGTTTGCAAAGGGTTTTACCTGAACAAAGTCAGCCTGCGGGGCATTAAACACCTCCAGGCAACTCCCAGGCCCTTCAGATCTTTCTGTGGGATTGGGCACTGGGCGATTGAACCTGTTCAGCTGCAAGAAGACCCAAAAGTGGGACGGAGCCAGAGAGAACAGCTTCTGGCCAGGGCTCTGCCAAGGGCTGAGCCAAGACAGACCTGGTGGAGACGCCAGGCTCGGGCCTGCTCCAACATTGTGGACACTATTTGTCAAGGCCCTTCAGTAAAACAATCAATCTGGGATTTAATATGTTGACTCAATCCAATGAGCATAGATCACTGGTCAGGATAACTCTGGCCGGATTTGCAGCAGGAATAAATGGAGGATCAAAAAAGAAAAAGTACCAAACGCCAAACCTGGTCTGGGCAGGTATAAAGTGTCCCCAGCAGGAGGGGTTTTCTGCCTGTTCCCTCGGCCAGAGCCCAGCTCAGAATTCCACCTGATGGGCCTGGTGTGTCTGGGGGATGATTCTGGCGACTTGTCAGCTCCTGAGCCCCGCTTTCCACTTGTAGTAAAGCAAAGTAGTAACCCCCACACCCCCTCTACAACATGTGCCCACAATGACAGCTGTTTTCGGGGTGGGCTTCCATCTCTGGTAGGCCTGGAAATCTGGATGCTTCCAGGATCCCGGCCACTTCACCCTGCCCCCTTTCCCTTGGTGTCAAATATATGCCAGTACTGTATTTGGTTTACCGAAAGGGTGGTTACATTCTGCTGTCTTCTGTGTGAATGAGGTTTTCACTTTCCTTAATTTTTAAAAACCACTTAATACCAAGGTTAGTTTAGTTGCCTCCACTAGCCTCATACCCTCCCCCCACAGGACCCTCTGGGGGGTCTTGTCAGACTTGGCAGGAACCAGCCAAACCCGGGCCCCCCAGGGTGGTGGAGGAAGAGAAATGTCCCTGGGTTAGGGAGGTTTGTCATTACCCATGACTGATGGGCTGCCTTGCAGTTCTCAGCCCTCACTTCTCCTTCCTCCACAG
Seq C2 exon
TGAAAACCAGGACGAAAGACAAATATCGAGTGGTGTACACGGACCACCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTACAGTCGCTACATCACCATCCGGAGGAAAGCCGAGCTAGCCGCCACGCTGGGGCTCTCTGAGAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165556-CDX2:NM_001265:1
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=0.569 A=NA C2=0.367
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
- 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)