RnoINT0033700 @ rn6
Intron Retention
Gene
ENSRNOG00000002974 | Cdx4
Description
caudal type homeo box 4 [Source:RGD Symbol;Acc:1561529]
Coordinates
chrX:74165187-74171880:+
Coord C1 exon
chrX:74165187-74165855
Coord A exon
chrX:74165856-74171734
Coord C2 exon
chrX:74171735-74171880
Length
5879 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
ATGTCATGCTTCTCCAACAGGGA
3' ss Score
9.33
Exon sequences
Seq C1 exon
AAGGTTGGAGTAGTCCGAGCCGCCCAGAGGAGCTGGCAGCACAGCGAGTGCTGACCCATTCATTGATAGCCTCTTGCATCTCAAACTCGGGTTGGCGCTAAGTTTACAGGGTCCTCAGGATGGCTTAGGGGGCAACTTCTTCTATCCAAGCCACCATGTATGGAAGCTGCCTTTTAGAAAAAGAAGCGGGAATGTACCCAGGCACTCTCAGGAACCCTGGAGGAGGCAGCACAGCCGGAGTGGGCACCTCTGGGGGCAGTGGTAGTCCTCTGCCTGCCTCCAACTTTACTGCAGCCCCAGTTTACCCACACTACATGGGGTATCCACATATGTCCAACATGGATCCTCACGGGCCTTCGCTGGGAGCCTGGAGCTCACCCTACAGTCCGCCCCGGGAAGACTGGAGTACATACCCTGGGCCGTCCAGCACAATGGGCACAGTGCCCATGAACGACATGACCTCGAGCTCCCCAGCTTTCGGCTCCCCAGACTACAGCACTCTGGGCCCCACTGGCGGTGCAGGCGGTGCAAGCAACGGCGGTAGCCTGCCAGACGCGGCCAGCGAGTCACTGGTTTCCATCGACTCAGGCACCTCTGGCGGCGCCACTTCTCCCAGCAGGAGCCGCCACAGCCCCTACGCGTGGATGCGCAAGACTGTGCAGGTGACCG
Seq A exon
GTGAGTAATCCATCGTTCCACTGTCTCTTCTCTTCTCTACTCTTGGTCCGCCTGCCCTCTTACTCTTCACTCTGCGTCCCGCAGAAGAGTTCAGCTAGGCAGCCCACGGGGCAACTGGCTGGCGGGATAAGTAATTTCCTCCTTTGTGCCTAGGTTCAAAGCTGGTTAAAAGCAGCGCTTGGAACTAAACCTTTCCTGGGGGTTTGTTGAGGTGGGCTTTTTTATTTGGTTATTTGGTTGTTTGGTTGATTAGGTTTGGTTCGGTTCGGTTTGGTTTGGTTTTTACCCTTCCCAGATAAGTCAAGGGAGTGAGGGCATGAACAGTGTTCCCGATGAACCACAAGGATCGGGATCCAATCCTGTCGTTGTCCGGAGGGAAAAACAGAAACACGTGTGATGAACGGGGTGAGAAGACAGTTAAGGTTGTCCCGGTGCTTGCCGGTTTTATGTCCAAATCGTCCCCTATCCTATTATGCAGCCTCGCTGAAAACTGGTGATGCTCAACTTAATAGGTGCTTAGCTGGCAAACGACGCCCCAGCCTATGAAGGCTTCCACGGCAAAACGGCCTCTTTACAAGACGCCCAAGGAAACTACAGCTTCCGTCGACCAAATTAGCACTGTCTTGAATAAAGCCTAACGCCTTTTTCCAATGTCCTACCCACTGAAGGAAGCGTTACAGCACTGAGCTGTCATTTCATAGGACACTATCCTTACACCCACCGTATTATTCACACCCCCCTCCAAGTGCCTAAAGCCCTCATCGCTAATTCAGCAGGTGGCCACAGATGCAGAAGCAGAATGCAAGTCTGCGACAGCGACAACACACAAGAAGCCATAAGGATCCCGTTTAAGGTCTAATGGCACTGACCAGCAAGCCCTGGTGGGCAGGCAACCGCTGGGGGGGTGTGCGGAGAGCTTCGAGGAAATGAGGACTCCACTATAATCTTGGACTAGGAGACGGTGACATGTTCGTTTTCAGCTGTGGTTGTTCTCCTAGCATTTTCTTATTCCAATACTTGATCCCTGTCATTAGAGAAAATTAGTGACATTTCCCTCTGGAGAGGCAATGATATTTCAATAGTATTTGTCCATGATGATATATACTCTTCACAACCCTTTGTTGTCCCTTCTCGCTCCTCCAAGAAGCAAAGGTGAAAGGGTTAGGGGGTACCATTTCCTACTGTTAGGAAACTTTTCAGCCACAAGGAGGATGTTCCAGGTCTAACTAGGGTACAGATCCCAAGTTAAAAGTAATCCTTAAGAACTTATATTAAAAAGAGGATATGGGTGAGTCATGTAACTTTAAAGACAAATGAGGCGAGGGTAGGGCATTCCTCCCCAGAGCTGTTCTTACATCTAATCTTCAGGGTAAAACTAACATCCATTCACCAAAACCTAAGAATAAGCAAAATACACATTTTTAAAAGGACATCAAAGAGCTACTGTCTAGGATTTTTCTTTGAAATACTGTGGGGAGGGGATGTCGCTAGCTTGGTTTTCAAAATGGAAAACTGTGAGGGAAAGAACACAGTAAGAAAATACGGTTGTGATGAATTGTCTTTGTGTTGCTGAGGGAAACATGACAGCTTTCTCTGTTTTGCTTTAAGAGGAAAGAGAGAGAGAGGGGGGGGGAGATCTCAGAGCCTCTTTGGGTAATTCTGATGCCAAGAGAAGTTGAGAAGGATCCCCATAGTCTGTGTGCCTTCATCTCTTCAGTGCTTAGGAGAAGTTTAAAACTGAGAATGATGTTACAGCTCCTTGGACTCTTGGCAACTTGTCCTATAGACAAAGTTTTACTAACATTGACATTTGTTTCATTTGAATTCCTCGTAAGTTAACACCACCCTTTTGCATGTTCTTGTAGGCTCAAGTTGCTATTTGTTGACAATTTGAGATGATGGTTGTGCATGAGAGCACCCCGCGCTACACACATAAGTGATGCTTTGCATAAGTTCTGGAGATTCTAGTCTCACTGAGTATCTTTCATAATACAGGGCCATAAACTTCACAAAAATAAATGCCATCACCCCGGGACACTCCGAATCAAAGTGTACCCCTTTATATGCTTAGCAAGGGAGCAGGTGTTAAACGTCTGTTAAGTGAATAGACAAGTTAGATCTTCCTAAGCTTTCTGTTCACCTTGTACCATCATTGCACATCAACCTATGGTTTAGGGCTGAGAGAGAAAAAAATCTATGGACAACAGACTGGACGTAGCTCTTCCCTGAATTAAGGCAATCCCATGAGAGCTTTTTTTTTTCCATTAATGAAGATAATTGAAACAGACTTAAGTTAAAATGTGTGTGTATGTGTGATATGTGTGAGTGTGTGTGTATGTGTGTGTTGCACTCCTTACAGCTATGATTTCTAAAGCAAGGAGATTGACATGTAGAATAAATCACTGCCTTCCAGATAATCTGATTTAAAAGGCTTTTATTTATTTTTATTTGGACATAGTTTTCTTTCTTTTTTCTTTTCTTTTTGGTTTTTTTTTTTTTTTTTTTTTGGTCCTTTGTGCAGCTCTGGCTGTCCTGGAACTAGCTCTGTAGACCAGGCTGGACTCGAACACACAGAGATCCACCTGTCTCTGCCTCTTGAGTGCTGTGTAGCTTTCTCAGTATTCTATTCCAAACACATGTCATTATATGCAATCTATCTTGTCCAAACATTTCTATCAAGATTAATATCTTCCAGCAGTCTCACAATTTAAATGCCAGTGTATGAGAACAAGCCATTTCCCACTGTTTTCTGTAGTAGAGAACTGTGGCCCTGTATGAATATTGGCCAGGCTGCATGCTAAGCAGAGCTGGAAACAGGCTTCCCTGTTTACAAAAGGAGAGGAAGTCATTTTGAGTGATTCTAATTAAGCCACTCACCACTAAGGAAATACTTTTAAAGCTGTATTCATAAACTGAATTGCTTAATAATCCTTGAAGCTTTTGCCATTGTCTTCCTTGGTTTTTCATGTTTTGTTGGACAATTTTTTTAAATGAGTTTGGATGTGATTTTTAGTTTTAAAGCAGTAAAGGATTGCCATTAGGGGAAAAGTCATCCCCGTGAACTGTCTGTGTAAGAAAACTGGCTGTCTCCCATCATTTTTCTCCATTGTCATCACCATTGTGATCCTGAGGCTTTGTACTGGTTCTTCTGCCTAATAGCACCTTGGCTGCTAGCCTCTCCATCAAACACTATTTCAACTATACTTATAGTGACAGTGTCATCTTATATAGTGAAATCACCTTATGAACTGTGCCCCCTGGGTGGTGGGAAGGACCACTGTGAACTATGAAGGTGATTGTTCAAATCTTTGTGGAAGAAGTAACAAAATTCTCATTTCACATGAGTGGAAGTAGCTCTTCAATAGACCTTTTTCTTAGACCTTTTTCCTAAATTAACTCACAATATCAGCTGAGAAGGAAATCCCCTGGTCTGAAAATGTCGTTGTCTCTGGAAAATAGAGGAAACTAAACAATAAGAACAAGTATTCCTCATGCTTTGCTGGTGTTTGGCTTTAGTTGTGGGAATATGGACTTTATGCTGTACCAGAAAGTGGCCAAATCCCTTCACTCACTTCAGGAGAACAGGGGGAAAGACATGGCTTCGAGAAGACAGCGCGAGACGAGATGGGTGCCAGGAAATTTCCATGTCTTTCTCTTTGTAAACTGTGCAAGTAGTATACTCTCCCTTGTCTTTGGGGTTTTCGTTCTTATCATCAGATTGGCCCTACAGATCCTTTTTAACACTTGTTCGGCTTTGATATGCATCTCCGCTCTTGTCACTGCCCCTTTCTTCGAAGGTTATATTGCCGGAAAGGGTGACCATTTTCATGGCAAATAAAGAGGCCTGGTCTTGACTTTATTGTCCTCAGAAGAAACTGCAAGAGGGGAATTTATGACCAATGGGGGTGGGGAAGGACCACAATGTTTCCAGAGTTCTTGAAGTCTGGTTATATTTACTGATTAATTGACTGAACCGAAGTCACAGACACACGCAAGTTGAATTTTAACCTCCCTGTTTCAAGTTAAAATTTAAACTCAGTCCCTTTTTTGATCAGGAAGGGTTTTAGGAACTAACTCCTCAAAGACATAATTTGATTCTAAAACTGAAGTCCTGAAAACAAATTAAACCTCAGGTTTTTGTTTTCATCCTTCATTATACATTCTGTCTTTGAAAGATGCCAAAAGCCTGACCCTTGGTTTTCTGTGTTTCTGCGGGAATCCAGAAATCTGGCTCAAAGTTTGGACCTTTGAGGAAAGTTAGTTGGCTGGGACTTAGGGCTCATCATTTCAAGGGAGGGAATTGCACTGAGTAGCCAGTTATCCAGCCATTTAGCGGAATCCTAAGGTAGATCTGTTTCAACATCCATGCCCCCTCCTCTTCCCGGAGATGAAAGGGTGTCTGACATTTGTTTAGGGCTTGTAAATTCCAAACCAATTGGTTGATGTTCCTGAATGTAAAGAGGGTTCAGGATGGGATCCATGCGATGTTGCTCCTTTGTTAGGCCTGGGCTGCATCTTAACACCTCAATGGAGTTTAGGGACCCACTTTAAAGAGGTCTTTGTCCTACAGGTCGGCCCCCCAAAACTTCACATCAAAAACAACCAAAGAAGATCAGAAGAACTTTCTAAAAGCCACAGAGAAAAAAAGCAAAATCCTAGAGGGGGTTAGAGAAACTGAAAGGAAAGGGAGACTTCCTAATCACCTTTGGAAAATTTGAAAGGAAGAATAAAACTCTATTTGAAGGCAAGCATGAGAAATTAACTAGATGTTGTAACACAAACCAAATGTTTGGATATCTTTTCAAAGCACGTGTAGTCCTCACTTCAGTCTGCTTAAGTCAACACACCCTCCTTTCCCCTATTCACTATTCACTTGGAAATAAAAAAAAAAAAAAAGCCTTAAGACTCCCACAGGAGAAATATTACTTTTTCTAATAAACATTAGGTGCTATTTTGAAACATAGTTTGCTAAGTAGCAATAAATATTTCTTTTCAAACTATACACATTCTTTCTAGGTAGTACACATAACTACAACATCAGGATTCCAGAATAGTTTACTGCATATGGGATTATACGTCCCAACAGGTTTAAACTGGGAATGAATCTAATATACTGAACCAAGAGTCAAAGGTTACATGCTTGGGTTTGCATGCCTAGGCTCACCAGCACAAATGCACTTACCTATACTTAACCTTAGGTTCTTTGTCCATACAATAACATTCTCTGCATAATTGAACAGAGTAGATAAGATAATGGGAAACAGTCGTGAAAGCATTGCATAAAATATAATTCATGAGGGCCAGGTGTGGTGGTGCACACCTTTAGTCCCAGTACTCAAGAGGCAGAGATGTGTGGATCTCTATGAGTTCAAGGGTAGCCTGGTCTACAGAGCAAATTCCAGGACAACCAGAACTATGCAAAGAAACCCTGTATCAAAACAACAGCAACAACAACACAGCAAGGTGTGAGTCATAGTGCCTGTTGCCATTATTGTTAACTCAGTTGTTATACGTGGATGGGGATGTAATGAAAACTGTGGGTTGAGTGTTTAAGTATTTTGATTGTTTTGGTATAACAGTAGGTCAATGGTAAAGTAGCTGTAATTTGACTGATTATTTCAGGAAAATATTAAAAGGGTTTTTGTTTCATATATATGATAGAATGGTGGATATTTATATCCACACCCACCTAGGTATAGATAACATGGCCACTTATGATAATGCATTTATGAAGAAATAGACATGACGTATTTGGTTTTAAAATGCAGTCCCTTTATATTTCAAAGTAGTAAATGAAAGTTAGAAGGGTAATTGGTTCCCTCAAACCAAACAATCTCCAGAAGAGAAGAATAAAATGAAATGTCATGCTTCTCCAACAG
Seq C2 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTGGTCTACACGGATCATCAAAGGCTGGAGCTGGAAAAGGAATTTCACTGCAATAGATACATTACCATCCGGAGGAAGTCAGAGCTGGCAGTTAACCTGGGCCTTTCTGAGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002974:ENSRNOT00000003973:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.814 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PU(97.5=92.4)
A:
NA
C2:
PF047317=Caudal_act=PD(1.8=6.1),PF0004624=Homeobox=PU(73.7=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]