HsaINT0032890 @ hg38
Intron Retention
Gene
ENSG00000131264 | CDX4
Description
caudal type homeobox 4 [Source:HGNC Symbol;Acc:HGNC:1808]
Coordinates
chrX:73453517-73455245:+
Coord C1 exon
chrX:73453517-73453662
Coord A exon
chrX:73453663-73454378
Coord C2 exon
chrX:73454379-73455245
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
GTGAAAATCTGGTTTCAGAATCGCAGAGCCAAGGAGAGAAAGATGATCAAAAAGAAAATCTCCCAGTTTGAGAATAGTGGAGGCTCGGTGCAAAGTGACTCTGACTCCATCAGCCCTGGGGAACTACCTAACACTTTTTTCACCACACCATCTGCTGTTCGTGGATTTCAACCTATTGAGATACAGCAGGTTATAGTCTCCGAATGAAAGAAAGCAAAGAGAAATTTAAAGTGCCCTTTTTTTAGTGATGTCTTTTGGGTCTCTAAGCTATCTACAGGGGAGTTGGAGCAGGGTGTAATTCCCTGTAAGGCAGTATTTGGAACAGATGGATGCACAATGGGTTGAAGATAATTTAGGGGACTCTTACTTTTAGAAACTATCCCCAGAAAACTCCTGTCACGTGCTGTGCTATATGTCAGTCACTCAGGAATCTTAGTGGTAAGGTATATAATTAAAAGCTAGAATCACAGGCCCTTCCAACTCTGTTCACAATTTCAGAAACTTGCTTATGAATAGACTGTAAAATACAATTTTGCCAGAAAGCACATTTGTGTATGTGTACTTCTGTTTGTTATTTGATGCTAGGTGTTTTCTTTTATGCTATCTTTAAGGAGTGAGAAGAAGGTAAACCGAAGTTTATCTATCTTTAGCTACCTTTCCAAGTGTTTAATTCAAAAGCTAACAGAATTTTTATAATAAGATAAATGTTTTAAAAATCATCAGAAGGTGATTCTGATTCCATTGTCACTGCTTAACAAGAATAACCAATAAAAAAGACAATTTTGGCCCTCAATCATACTTGTCTGGCATCAATTATCTCAGAACTTTCAACTTGCAGTGTCATTTTAAAATCTTGTCAAAACAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131264:ENST00000373514:2
Average complexity
IR
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGAGCTGGCAGTTAACCTG
R:
GGGAATTACACCCTGCTCCAA
Band lengths:
342-1058
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