HsaINT0032890 @ hg19
Intron Retention
Gene
ENSG00000131264 | CDX4
Description
caudal type homeobox 4 [Source:HGNC Symbol;Acc:1808]
Coordinates
chrX:72673353-72674421:+
Coord C1 exon
chrX:72673353-72673498
Coord A exon
chrX:72673499-72674214
Coord C2 exon
chrX:72674215-72674421
Length
716 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
GTTGCCCCATTGTGTTTCAGGTG
3' ss Score
10.52
Exon sequences
Seq C1 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTAGTTTACACTGATCATCAAAGATTGGAGCTGGAAAAGGAATTCCATTGCAATAGATATATCACCATCCAGAGAAAATCAGAGCTGGCAGTTAACCTGGGCCTTTCCGAGAGACAG
Seq A exon
GTACACCAGAAGTATATCCAACATGTCCCGTATAGTCCATTTCAATAGAATCAGAATTCTAGAATTGTAAAGTCCCTTAATGCATTGCCTTATCCCAAGTAGCTTGCATTTCAACCACGTGTGAAGGCACATTGATATCGCTCTCTTCTATCTCCAGCAAGAGATATAAAATATTTCATCACCCTTGTTCTCTCATTTATGTGTTTCATTAATATTTTACTAATAGGAAGACAAACTTCTTATTAGTAATAGTATACTAATAGGAAGATAAATTTTCTATTTTATTTTATTAATATTATACTAATAGGACGTTTCTCTTTAGTGAAATATTAATAAAACATAGAAATGGTTGATTATAATTACCTTTGCTATTTAAATCTCTCTCTCTTATCAGCACACCTCAGCTTCTGTCATTCCAGCATTATTTATTTCTACCTGTGCAACAGAGGAGGTGGGTAAGGTATAATATTAAGATTATTGCATTCAGAGTTAGTAGCCCTAGACTTGGATCTCAGTTTCATTTCATGCAAGGTACTTGCCCTCTCTAAGTCTCAAGCTTTTTTTCTAACCTGTTAAGTGGGCATACTTCACAAGGTCATTGTGAGGCTGAAATGAAGTGATGCATATGAAAGGGCTTTGTAAATGCTAAAGTCTCTGTACAATATCAGAAATCACTAAGTTAACTGCATTCAGTATGTTGCCCCATTGTGTTTCAG
Seq C2 exon
GTGAAAATCTGGTTTCAGAATCGCAGAGCCAAGGAGAGAAAGATGATCAAAAAGAAAATCTCCCAGTTTGAGAATAGTGGAGGCTCGGTGCAAAGTGACTCTGACTCCATCAGCCCTGGGGAACTACCTAACACTTTTTTCACCACACCATCTGCTGTTCGTGGATTTCAACCTATTGAGATACAGCAGGTTATAGTCTCCGAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131264-CDX4:NM_005193:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.324
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(1.9=6.1),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
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAGGACAAAAGAAAAGTATCGTGT
R:
TCGGAGACTATAACCTGCTGT
Band lengths:
344-1060
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)