HsaINT0032888 @ hg19
Intron Retention
Gene
ENSG00000165556 | CDX2
Description
caudal type homeobox 2 [Source:HGNC Symbol;Acc:1806]
Coordinates
chr13:28536278-28539152:-
Coord C1 exon
chr13:28539007-28539152
Coord A exon
chr13:28537507-28539006
Coord C2 exon
chr13:28536278-28537506
Length
1500 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
CTCCACCTTTCCATTTCTAGGTT
3' ss Score
11.7
Exon sequences
Seq C1 exon
TGAAAACCAGGACGAAAGACAAATATCGAGTGGTGTACACGGACCACCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTACAGTCGCTACATCACCATCCGGAGGAAAGCCGAGCTAGCCGCCACGCTGGGGCTCTCTGAGAGGCAG
Seq A exon
GTGGGGACCGCCTAGCTCCCTCCGGGCGGGCCACTGCCTGGCAGAGGACCATGAGAGTTAGAAAATCTGGCTGCAGGGGCCATCTAAATCTGTGGAGAGACTGAAGCAGGAGGATGCAAGCATTCGTCTTTGGAGTCCTTTTTTTTTTTTTTTTTTTTTTTAAACAGAGATGGGGTCTTGCTTTGTGGCCCAGGCTGGAGTGTAGTGGCACAATCATAGCTCACTGCAGCCCTGACTTCCTGAGCTGAAGGGATCCTCCTGCCTCAGTCACCTGAGTAGCTTGGACTACAGGCTCGAGCCACCATGACTGGCTAATGTTTAAATTTTTTGCAGAGATGGTCTCACTGTCTTACCCAGGTTGGTCTCAAACTCCAAATGCTCCTCCTGTCTTGGACTCCTAAAGTGCTGAGATTACCGGTGTGAACCACCATGCCTGGCCTGGAGTACATGCCCCCCCACCCGCCACCGTCGAAACGCAGTTTCACTCTTGTTGTGCAGGCTGAAGTGCAATGGCGCGGTCTCAGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCTTCAGCCTCCCAAATAGCTGGGACTACAGGCATGTGCCACCACGCCCGGCTAATTTTGTATTTTTAGTAGAAATGCGGTTTCTCCATGTTAGTCAGGCTAGTCTCGAACTCCTGGCCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGAGATTACAGGTGTGAGCCACTGTGCCTGGCCCTGGAGTACTTTTTTAAAAAGCCTCCTTCTACCTTTAGTCCTCTTTTTTTGATGTTGTTGATTTTTTCTGTCTCTCTCTTTTGAGGGATATAAGAAGTGTGAAAAACAGCCAAGGGTATTAGTTTAATCCAGAATTCCATTTGGGTCTATAAAGACATATTAAAGACCTATTCTCTTTGTTTCCAGCACTGTACCTAAGAAAATAAACTGAATAAAGTACTCAGTCTCTCACAAAAACTAGAGGGACAAGACTTGGTTCATGAACATTTTATATATATAGTCTAGAAAAACAGGCCAACTTCACAGCCAGGAAGCCACAAAATTAAATCTCATTTTCAGCTCTAAGGTGAGGAAAATTACGTTTTAGTTTAGCCTTGAGGGGCCAAAGGTTGCCATTTGAAGTATACCACCCAGCACTGGCCTCCCTTTGCTGTGTAGAAAGGGCCTTGCAGTTTCAGTTTTCCTTGGTTCTGAGACTTTAAACTTTTGCAGTAAATACGTAGATAAAAGTTGCTTTGAAAAGAAACTCAGGGAGCAAGGAAGGAGGAAGACTCTTCCCCATGAGGCTGAATTGGGCCTAAGAATGGATCCAGGGTTGGGCTGTTATGGGGATGCCCGAGGAAAGCTTCTAGAAGGACTTGGAGTTCTGTAGCTGGAGCAGAAGATGTTGATGATACTGCTGGGTACTGTTCCTCTTTTCCCTCACATCTTCACCACAATGTGCTTTTCTCCACCTTTCCATTTCTAG
Seq C2 exon
GTTAAAATCTGGTTTCAGAACCGCAGAGCAAAGGAGAGGAAAATCAACAAGAAGAAGTTGCAGCAGCAACAGCAGCAGCAGCCACCACAGCCGCCTCCGCCGCCACCACAGCCTCCCCAGCCTCAGCCAGGTCCTCTGAGAAGTGTCCCAGAGCCCTTGAGTCCGGTGTCTTCCCTGCAAGCCTCAGTGCCTGGCTCTGTCCCTGGGGTTCTGGGGCCAACTGGGGGGGTGCTAAACCCCACCGTCACCCAGTGACCCACCGGGTTCTGCAGCGGCAGAGCAATTCCAGGCTGAGCCATGAGGAGCGTGGACTCTGCTAGACTCCTCAGGAGAGACCCCTCCCCTCCCACCCACAGCCATAGACCTACAGACCTGGCTCTCAGAGGAAAAATGGGAGCCAGGAGTAAGACAAGTGGGATTTGGGGCCTCAAGAAATATACTCTCCCAGATTTTTACTTTTTCCCATCTGGCTTTTTCTGCCACTGAGGAGACAGAAAGCCTCCGCTGGGCTTCATTCCGGACTGGCAGAAGCATTGCCTGGACTGACCACACCAACCAGGCCTTCATCCTCCTCCCCAGCTCTTCTCTTCCTAGATCTGCAGGCTGCACCTCTGGCTAGAGCCGAGGGGAGAGAGGGACTCAAGGGAAAGGCAAGCTTGAGGCCAAGATGGCTGCTGCCTGCTCATGGCCCTCGGAGGTCCAGCTGGGCCTCCTGCCTCCGGGCAGGCAAGGTTTACACTGCGGAAGCCAAAGGCAGCTAAGATAGAAAGCTGGACTGACCAAAGACTGCAGAACCCCCAGGTGGCCTGCGTCTTTTTTCTCTTCCCTTCCCAGACCAGGAAAGGCTTGGCTGGTGTATGCACAGGGTGTGGTATGAGGGGGTGGTTATTGGACTCCAGGCCTGACCAGGGGGCCCGAACAGGGACTTGTTTAGAGAGCCTGTCACCAGAGCTTCTCTGGGCTGAATGTATGTCAGTGCTATAAATGCCAGAGCCAACCTGGACTTCCTGTCATTTTCACAATCTTGGGGCTGATGAAGAAGGGGGTGGGGGGAGTTTGTGTTGTTGTTGCTGCTGTTTGGGTTGTTGGTCTGTGTAACATCCAAGCCAGAGTTTTTAAAGCCTTCTGGATCCATGGGGGGAGAAGTGATATGGTGAAGGGAAGTGGGGAGTATTTGAACACAGTTGAATTTTTTCTAAAAAGAAAAAGAGATAAATGAGCTTTCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165556-CDX2:NM_001265:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.367 A=NA C2=0.905
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=15.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGCTACATCACCATCCGGAG
R:
TCAGCCTGGAATTGCTCTGC
Band lengths:
358-1858
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)