HsaINT0032886 @ hg19
Intron Retention
Gene
ENSG00000113722 | CDX1
Description
caudal type homeobox 1 [Source:HGNC Symbol;Acc:1805]
Coordinates
chr5:149562331-149564121:+
Coord C1 exon
chr5:149562331-149562476
Coord A exon
chr5:149562477-149563036
Coord C2 exon
chr5:149563037-149564121
Length
560 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
TCTGTCCTCCAACCCCACAGGTG
3' ss Score
10.45
Exon sequences
Seq C1 exon
GTAAGACTCGGACCAAGGACAAGTACCGCGTGGTCTACACCGACCACCAACGCCTGGAGCTGGAGAAGGAGTTTCATTACAGCCGTTACATCACAATCCGGCGGAAATCAGAGCTGGCTGCCAATCTGGGGCTCACTGAACGGCAG
Seq A exon
GTGTGTCTGTCTTCCTATCTCAGCCATAGGAGCAGTGCGAGGACTCTGGTCTCCAGGCTGCCAGGCAGAGTACAGAGCTCAGTAGAAGGAAAACAGAGAGGTTGAGTCTCCAGGCCATTGTCACACAGCACAGCAGAAACTGAGGTGCTACCAGCACCCTCCCTTAACAAAACCCAGTATCCTTGCCCCCAAAGGCAGGGGTAAGGGGATCTGATTAGCCACAGGCTACAGCAGGCTATTATTAGTGCTGTAGGAGGTGCACGTGCTATTTACATTAGGGGAGCAGTCACAGGGATAACAAGGAAGGCTTCCTGGAAGAAGTGTGGCCTGGGAAGATGGAGAGGGGGAAGGTTACAAAGAAGGGCATCTCCAGGGTAGGGGTGCAATGTCTAGAGGGGGAGAATGAATTCAGGGTCCATGTGGTCTGGGAGGCTGGAGAGGAGATAAGCCACAAAGCCACATGGAGAAATAGGGGCTCACTGTCCTCGTCTCTCCTTCTTGCACTCTCTCTTTCACTCTCTCCCTGCTGCCCACTCCATCTCTGTCCTCCAACCCCACAG
Seq C2 exon
GTGAAGATCTGGTTCCAAAACCGGCGGGCAAAGGAGCGCAAAGTGAACAAGAAGAAACAGCAGCAGCAACAGCCCCCACAGCCGCCGATGGCCCACGACATCACGGCCACCCCAGCCGGGCCATCCCTGGGGGGCCTGTGTCCCAGCAACACCAGCCTCCTGGCCACCTCCTCTCCAATGCCTGTGAAAGAGGAGTTTCTGCCATAGCCCCATGCCCAGCCTGTGCGCCGGGGGACCTGGGGACTCGGGTGCTGGGAGTGTGGCTCCTGTGGGCCCAGGAGGTCTGGTCCGAGTCTCAGCCCTGACCTTCTGGGACATGGTGGACAGTCACCTATCCACCCTCTGCATCCCCTTGGCCCATCTGTGCAGTAAGCCTGTTGGATAAAGACCTTCCAGCTCCTGTGTTCTAGACCTCTGGGGGATAAGGGAGTCCAGGGTGGATGATCTCAATCTCCCGTGGGCATCTCAAGCCCCAAATGGTTGGGGGAGGGGCCTAGACAAGGCTCCAGGCCCCACCTCCTCCTCCATACGTTCAGAGGTGCAGCTGGAGGCTGCTGTGGGGACCACACTGATCCTGGAGAAAAGGGATGGAGCTGAAAAAGATGGAATGCTTGCAGAGCATGACCTGAGGAGGGAGGAACGTGGTCAACTCACACCTGCCTCTTCCTGCAGCCTCACTTCTACCTGCCCCCATCATAAGGGCACTGAGCCCTTCCCAGGCTGGATACTAAGCACAAAGCCCATAGCACTGGGCTCTGATGGCTGCTCCACTGGGTTACAGAATCACAGCCCTCATGATCATTCTCAGTGAGGGCTCTGGATTGAGAGGGAGGCCCTGGGAGGAGAGAAGGGGGCAGAGTCTTCCCTACCAGGTTTCTACACCCCCGCCAGGCTGCCCATCAGGGCCCAGGGAGCCCCCAGAGGACTTTATTCGGACCAAGCAGAGCTCACAGCTGGACAGGTGTTGTATATAGAGTGGAATCTCTTGGATGCAGCTTCAAGAATAAATTTTTCTTCTCTTTTCAAAAATGTATAAAAATCATTATACATAGCATTAAAGAAACATTTTTGAGAAGTACAAATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113722-CDX1:NM_001804:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.897
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.8)
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:
CCAATCTGGGGCTCACTGAAC
R:
ACTGTCCACCATGTCCCAGAA
Band lengths:
354-914
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)