BtaINT0035991 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001726 | CDX4
Description
caudal type homeobox 4 [Source:HGNC Symbol;Acc:HGNC:1808]
Coordinates
chrX:82550494-82552068:-
Coord C1 exon
chrX:82551923-82552068
Coord A exon
chrX:82550679-82551922
Coord C2 exon
chrX:82550494-82550678
Length
1244 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
CAAAGCATTTTTTGTTTCAGGTG
3' ss Score
8.72
Exon sequences
Seq C1 exon
GGAAAACCAGGACAAAAGAAAAGTACCGCGTAGTTTACACAGATCATCAAAGGTTGGAGCTGGAGAAAGAATTCCACTGCAATAGATATATCACCATTCGGAGAAAATCAGAGCTTGCAGTCAACTTGGGCCTTTCTGAGAGACAG
Seq A exon
GTACACCGGAAGTGCATTTAACATTTTTCATATAAGCATTTCAAATAGGCTAAGATTTTAAGGACATCTGTAAGCAGGAGGGAAGCAAAAGAAGACTAAGCCATTCTCAAAGCTTTCCTAAAGCCCATATTTTTCCTATTGAACCTCCTAGTGTGGTGGGCACTATATAGGTGTGGAAACAAGGATGGGGACATAGTGGATGGAGAAGGATTAAAATCCCCATACAATTGGTCAGCCAAGTCAAAACCTTGATATGATTTCCCAAGTAGTTATAATCTATGTGTGAAGTTGAAATCTGTCAATCATGGCAATTATCTGGCTTATATCAGTCAAACTGTAACAGTAAATGAACACCAATGCTTATACCTGAATCAAGTTTTTCTATTATTCAGGCTAGGAGATTTAATTTTCTGTGGTCTATGTAATCCTATGATTCCTGCCTCAGATTTAGCTTACTGTGGATACTCAGTGAAAATTAAATCTTGGCAAGAATCAGTAGTTTCCACTCACCCAGCTTTTGACATGACATAACTATTTGATGTTCTTTTTTTTTTTCCACAAAGGTCTAGGAGTAATCCTGGATATCATATAATTCTAGAACTGTAAAGTCCATTAATGCCTTATCCCAAGTAATCTACATTTCAACCATTTATAAAGGCACACAGCAAGAGATATAGTACTTCATAACCCTTGTTCACCCAGTTCTGTGTCATTAAACTTACTTTAAAAAAAAAAATTTACATGGCATGTAGGATCTTAGTTCTCAGACCAAGGGTCAAACCTGTGCCCCGTGCATTGGAAGTGCAGAGTCTTAACCTCTGGACTGCCAGGGAAGTCCCTAACCTTAGTCTTTTAATGACAGATCATAATCACCGTTGCTATTTAAATCCCTCCCTTTTCATCACCATGCCTCAGAATCTGCCATACTATCATTATTTATTTTTACCTGTGCAACAAAGATGGTGAGTGAGGTATAATGTAAAGACTACTGCATTCAGAGTCTGAGGCCCTGGGCTTGATTTCAATTTCATCTCATGAAAGATATTTTCCCTTTCTGAGTCTCAGCTTTTTTAAAAACCTGTTGTCAAAAGGGCATACTTCACAAGGTCATTGTGAGGCTCAAGTGATGCATGTGAAAGAGTTTGTAAATATTAATACTAAAGCCCCAGAACAATATCAGCAATGACTTTGAAAAATGCATTCAGTATGTTGTCCCATTAAATCCAAAGCATTTTTTGTTTCAG
Seq C2 exon
GTGAAAATCTGGTTTCAAAATCGCAGAGCCAAGGAGAGAAAGATGATCAAAAAGAAAATATCCCAGTTTGAGAACAGTGGAGGCTCAGTGCAAAGTGACTCTGGCTCCATCAGCCCTGGGGAACTACCTAATATTTTTTTCACCACCCCATCTGCTGTCCGTGGATTTCAGCCTATCGAGATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001726:ENSBTAT00000002260:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.210
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=21.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAAACCAGGACAAAAGAAAAGT
R:
CTCGATAGGCTGAAATCCACGG
Band lengths:
326-1570
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]