RnoINT0033701 @ rn6
Intron Retention
Gene
ENSRNOG00000002974 | Cdx4
Description
caudal type homeo box 4 [Source:RGD Symbol;Acc:1561529]
Coordinates
chrX:74171735-74173347:+
Coord C1 exon
chrX:74171735-74171880
Coord A exon
chrX:74171881-74172973
Coord C2 exon
chrX:74172974-74173347
Length
1093 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
TAAAGCATTTTGTTTTTCAGGTG
3' ss Score
9.17
Exon sequences
Seq C1 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTGGTCTACACGGATCATCAAAGGCTGGAGCTGGAAAAGGAATTTCACTGCAATAGATACATTACCATCCGGAGGAAGTCAGAGCTGGCAGTTAACCTGGGCCTTTCTGAGAGACAG
Seq A exon
GTATTACCAAGCACTCCCACATATCACTTCAATTGCCTGGGGTTTGTAGAAAATAGCAAAAGAGAAGCAGATGCTTTTCTAGGAGCTCCTAAGCCCATACTCACCCTGTATTGTTTCATTGGCCAGAGGGTTTATTAACTATTGAATGGGTATGTGGACCTGGGAGTAAGAGAGCAAGCAAAGAGGTGCAAAGAAATTAGAAGTCCAATAGAATTCATCAATCAGGTCAAACTTTGATCTGGTCCCTCAAGTAGTACTAACAAGTGTGAGAAGTGGAAATTTCACAACTATGGCTGCTGTCTGCTTCCTATCAGTCAAACTACAAGAGGTACTGCACACCAGTGCAGTTCCATGGATGGAGCTTTTCTGTCATTCAAAATAGGAAATGTAATCTTCTCTAATCTGTATGATGTTATGATGCCTGCCTTGAATCTAGCTTATTGTAAACATTCAATGAAGATCAAGTTACAGCAAAGGTCAGCAGTCTCCACTCATTCAGACTTGGCAATTACATGAGCACCTGGTGATGTTTCCCTAAGTCTAGGAGTGATGCTGGAATCATAGAAGTCTAGAAATGTAAAATCCATTGATGTGTTGCCTTATCTCAAGCAGTTTGCATTCCAACCACATATAGGCACATTAAGACCACTCTCGTGTGGATTTCCAACAAGAAATAGATGGTATTTCATGACCCTGTTCACCTAGTTCTGGGTGTTAACTTTTTAATATAAGGAACTGTCTCTTAATGACCAACTGTAATCACTGTTGCTATTTGAATCCTTCTCTTTCATCAGCAGTCCTCGGCGTCATTATATAATTATTTCTACTTGTGTAATAGAGGATGCAAGTGACTTGGAATATATAGAGCTCTGCCTTCAGAGTCAGTAGTCCTAGGTTTGATGACTTCAGTCTCACTTCTTACAAAGCGCCTGCCCTCGCTGAGCCACAGTGTTTTAGAACCTGTAAAAGGGGTATAGTTCACAAAGTCACCCTGAGGCTCAAATGAAGTGATGTGTGTGAAGGAGCCTTGTAAGACCCACACTAGCCACTTAGGGTATTGTCCCCACTAAGTATAAAGCATTTTGTTTTTCAG
Seq C2 exon
GTGAAAATCTGGTTTCAGAATCGCAGAGCCAAGGAGAGGAAGATGATCAAAAAGAAAATCTCCCAGTTTGAGAACAGTGGAGGTTCCGTGCAAAGTGACTCTGGCTCCATCAGCCCCGGAGAACTGCCTAATGCTTTCTTCACCACTCCATCTGCTGTCCGTGGGTTTCAGCCAATTGAGATACAGCAGGTCATAATTTCTGAATGAAACGGGAGCAGAGAAACCAACGCATCCTTCCTGTTACAGTGTCTCTTTGGCCTCTAAGATAACAGCAGGGCAGTTGAGATCGGATATACTTCCTTATAAGGCACAATTCCAAACAAGTAGACACACCATGAGTTGGAGATATTTCAGAAGACTCTAATATTAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002974:ENSRNOT00000003973:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.309
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(1.8=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
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACGGATCATCAAAGGCTGG
R:
ATGCGTTGGTTTCTCTGCTCC
Band lengths:
342-1435
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]