RnoEX6058918 @ rn6
Exon Skipping
Gene
ENSRNOG00000060334 | Cdx1
Description
caudal type homeo box 1 [Source:RGD Symbol;Acc:621233]
Coordinates
chr18:56338336-56355341:-
Coord C1 exon
chr18:56355012-56355341
Coord A exon
chr18:56339040-56339185
Coord C2 exon
chr18:56338336-56338566
Length
146 bp
Sequences
Splice sites
3' ss Seq
ATTGCCCTTCTGCTCCTCAGGTA
3' ss Score
9.17
5' ss Seq
CAGGTATGT
5' ss Score
9.8
Exon sequences
Seq C1 exon
CCCCGCAGTACCCCGACTTCGCGGGTAACACGCACGTGGAGCCGGCACCCGCGCCCCCTCCGACATGGACTGCGCCCTTCCCTGCGCCCAAGGACGACTGGGCAGCTGCATATGGTCCGGGCCCCGCGGTCCCCGCCGCCAGCCCGGCCCCGCTGGCCTTCGGGCCCCCTCCGGACTTTAGCCCAGTGCCCGCGCCTCCCGGTCCTGGTCCTGGCATCCTGGCGCAGTCCCTCGGGGGTCCGGGAGCACCGTCCTCGCCAGGAGTGCAAAGGCGGACGCCCTACGAATGGATGCGGCGCAACGTGGCAGCTGCAGGCGGCGGTGGCAGCG
Seq A exon
GTAAGACTCGGACCAAGGACAAGTACCGCGTGGTCTATACAGACCACCAACGTCTAGAGCTGGAAAAGGAGTTTCACTACAGTCGGTACATCACCATTCGGCGCAAGTCAGAGCTGGCTGCTAACTTGGGTCTCACAGAGCGGCAG
Seq C2 exon
GTAAAGATCTGGTTCCAGAACCGTCGGGCCAAGGAGCGTAAAGTAAACAAGAAGAAACAGCAGCAGCAGCAGCAGCAACAGCAGCAGCCCATGCCTCCCACACAGTTGCCCCTGCCCCTGGATGGCACCCCCACACCATCGGGGCCACCCCTGGGGAGTCTATGCCCCACCAATGCTGGTCTTCTGGGCACCCCCTCCCCAGTGCCGGTCAAGGAGGAGTTTTTACCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060334-'1-2,'1-1,2-2=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=0.327 C2=0.947
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(80.0=97.3)
A:
PF0004624=Homeobox=PU(73.7=85.7),PF119313=DUF3449=PU(44.8=79.6)
C2:
PF0004624=Homeobox=PD(22.8=16.9),PF119313=DUF3449=PD(52.9=59.7)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGCCAGGAGTGCAAAGG
R:
GCATTGGTGGGGCATAGACTC
Band lengths:
253-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]