RnoINT0033699 @ rn6
Intron Retention
Gene
ENSRNOG00000032759 | Cdx2
Description
caudal type homeo box 2 [Source:RGD Symbol;Acc:621234]
Coordinates
chr12:9467817-9469724:+
Coord C1 exon
chr12:9467817-9467962
Coord A exon
chr12:9467963-9469112
Coord C2 exon
chr12:9469113-9469724
Length
1150 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TCTATTTGTGTCATTTTTAGGTT
3' ss Score
11.84
Exon sequences
Seq C1 exon
TGAAAACCAGGACGAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAATTTCACTATAGTCGATACATCACCATCAGGAGGAAAGCTGAGTTGGCCGCCACACTCGGGCTCTCGGAGAGGCAG
Seq A exon
GTGGGAATCACCTTCCCTGGGTCTGGCTATTATGGCCTGGGGCGATCCTCGTGGGTAGCACTGGAAAACCCACCTGGTCCAGGGAGCCGTCGCCTTTTGAGAGCCCTTGGGGTCTCCGTTGTTTTTCCTGCTCTTTCTGTGCTTTCTATTTCGATGGATCTGGAGAGTGGCAAGGGAAAAGCCAAGTCGACGCTGCCGCTGCCGCGCGGTGGGGCTTCACTTGGCCGGATAAAGAGCGAGCTGTGGGGGCTGGGGATTTGGCTCAGTGGCAGAGCACTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGACCCAAAAAAAAAAAAAAAAAAAAAAAGAGCGAGCTGTGGAAGGGTGGTTCTCAACATGTGGGTCTCGACCCCCTCGGCTCCCCAATAGCAGAATTACAGTTATGAAGTAGCAATGACAATGATTTATGGTTGGGGAGTCACCACAACGTGAGGAACTGTCCTAGAAGAAAAGCACAAAGGTCCAGTCTACTCATACACACTAAAGAGGCAGTGCTCTTGCAGAGAACCAGAATTCCGTTTCCAGCGCCTACATCAGGTGCCTCACGGTGCTGTGTAACTCCAGTTGCAGGGGCCCTTCCAGTGCCTCTGGCTTCTGGCGATGCATGCAGATATATACAGACACATACACATATCACAAATTAAAAAAACAAACCCTTGAACTTTTTTTTTTTAAGAAAGCAAAAGAAGCCCTAGTCAGCACCTGAACACTTTCTGTAGTCCAGGGAAAAGGAAAAATAAAAAATAAAAAACAGGACAAATTCATAGCCGGAAAGTTTTGGATGAAATTTGGTCTGTGCCATGGTGAAGACCATCGCAGTGCGCCCATGAGCTGTGAGGACCAAAGGGTGACACATGGGGCACACCTGAGCTGGCCAGCCGATTCGTGTAGGGAATGACTTTCAGCATGGTTCCATTCCTTGGTTTTGAGGTTCTGTTTCCAGTCAAGTTTAGAAAGCAACTTGGGGAGGTGGCATGGAGAGGAGGCTGAACTGGCTTTGGGAACACTTCTAGCACCGAGTTGACGCTCGGTGGAGGGAGGGCGATCTGGGTGACACATTTCCCGGTTAATATCTTCTACCTTCTATTTGTGTCATTTTTAG
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAAAGGAAAATCAACAAAAAGAAGTTGCAACAGCAGCAGCAGCAGCAGCCTCCCGCACCGCCGCCACCACAGCCTTCCCAGCCTCAGTCCGGTGCATTGCGGAGCGTGCCGGAGCCCTTGAGTCCTGTGACCTCCTTGCAAGGCTCGGTGCCTGGTTCTGTTCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAACTCCACTGTCACCCAGTGACCCCTCCTGTGGCCTGAAGTGGCGGTGGCTCAGCAATCCCAGGCTGAGCCATGAGGAGCACGGACACTGTGAGAAACCTCAGAAGAGACCCCTCTTCTCCTACCCACAAACAACACCTACAGATGGAGATCGAGGACAGAGGGCAGAAGACGAGTGGGATTGTGGACCTCAGGAGAAGATATGGTTTAGATTTTTTTTTTTAAATTTTTCCCGTTCTGACTTTTCCTGTCAGCAAAGGAAGTGATTCCTGGGGCTTCTTCATTCATGCTCCTTGCCAGGACTGGCTACAGGCACCAAGCTTTCAGCTTCTTTTGCCTCAGCTCTTTGCCTCCAAAAAAAAAGAGACTGTATTTCTGTTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032759:ENSRNOT00000048188:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTACACAGACCATCAGCGG
R:
TTTAAAACCCCTCCAGCTGGC
Band lengths:
344-1494
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]