RnoALTD0006186-1/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000032759 | Cdx2
Description
caudal type homeo box 2 [Source:RGD Symbol;Acc:621234]
Coordinates
chr12:9467817-9469724:+
Coord C1 exon
chr12:9467817-9467958
Coord A exon
NA
Coord C2 exon
chr12:9469113-9469724
Length
0 bp
Sequences
Splice sites
5' ss Seq
GAGGCAGGT
5' ss Score
1.9
3' ss Seq
TCTATTTGTGTCATTTTTAGGTT
3' ss Score
11.84
Exon sequences
Seq C1 exon
TGAAAACCAGGACGAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAATTTCACTATAGTCGATACATCACCATCAGGAGGAAAGCTGAGTTGGCCGCCACACTCGGGCTCTCGGAGAG
Seq A exon
NA
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAAAGGAAAATCAACAAAAAGAAGTTGCAACAGCAGCAGCAGCAGCAGCCTCCCGCACCGCCGCCACCACAGCCTTCCCAGCCTCAGTCCGGTGCATTGCGGAGCGTGCCGGAGCCCTTGAGTCCTGTGACCTCCTTGCAAGGCTCGGTGCCTGGTTCTGTTCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAACTCCACTGTCACCCAGTGACCCCTCCTGTGGCCTGAAGTGGCGGTGGCTCAGCAATCCCAGGCTGAGCCATGAGGAGCACGGACACTGTGAGAAACCTCAGAAGAGACCCCTCTTCTCCTACCCACAAACAACACCTACAGATGGAGATCGAGGACAGAGGGCAGAAGACGAGTGGGATTGTGGACCTCAGGAGAAGATATGGTTTAGATTTTTTTTTTTAAATTTTTCCCGTTCTGACTTTTCCTGTCAGCAAAGGAAGTGATTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032759-5-2,6-2-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.902
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=15.7)
Main Inclusion 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:
TCACCATCAGGAGGAAAGCTGA
R:
TTTCCTTTCCTTGGCTCTGCG
Band lengths:
94-98
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]