RnoINT0033698 @ rn6
Intron Retention
Gene
ENSRNOG00000032759 | Cdx2
Description
caudal type homeo box 2 [Source:RGD Symbol;Acc:621234]
Coordinates
chr12:9464026-9467962:+
Coord C1 exon
chr12:9464026-9464672
Coord A exon
chr12:9464673-9467816
Coord C2 exon
chr12:9467817-9467962
Length
3144 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
AACTTCTCCTTCCTCCACAGTGA
3' ss Score
9.26
Exon sequences
Seq C1 exon
CAGTAATCAGCTACCTTTATCCCTAGCCCCCTGCGCCCCGCGCCCTTGGCAGCCTTCAACGCTTGTCCCCAGGCAGTATGGTGAGGTCTGCTCTGGGTCCCTCGCCACCATGTACGTGAGCTACCTTCTGGACAAGGACGTGAGCATGTACCCTAGCTCCGTGCGCCACTCCGGCGGCCTCAACCTGGCGCCGCAGAACTTTGTCAGTCCCCCGCAGTACCCGGACTACGGTGGTTACCACGTGGCGGCCGCCGCTGCTGCGGCGGCGAACTTGGATAGCGCTCAGTCCCCAGGGCCATCCTGGCCCACCGCGTACGGCGCCCCTCTCCGCGAGGACTGGAATGGCTACGCACCCGGGGGCGCTGCCGCAGCCAACGCGGTAGCCCACGGCCTCAATGGTGGCTCCCCGGCCGCCGCTATGGGCTACAGCAGCCCCGCCGAATACCACGCACACCATCACCCGCATCATCACCCTCACCATCCGGCCGCTGCGCCGTCCTGCGCCTCCGGATTGCTGCAGACGCTCAACCCCGGCCCTCCAGGGCCCGCAGCCACCGCCGCCGCAGAACAGCTGTCCCCCAGCGGCCAGCGGCGAAACCTTTGTGAATGGATGAGGAAGCCAGCTCAGCCGTCCCTAGGAAGCCAAG
Seq A exon
GTATGCGGTGCTGGGGCGCGCCCCTGGTCCCGCGCGTGTGGGGGCTGTCTGCCAGCTCCTAGACAGGACAGGAGAAGGGACAAGGGGAGAAATATGGGGGTGGACCCCTGGGGGACTCATCCCAGGAGTGTATATTTGTGCCTCGCACCCCCAGGTTTGTTTAGGGCAGAAGAGTGATTTCTTCCTCTTTCTAACTGTACCTCGTTGGCAACCTCGGGACCCCTTCGGAAGCTCCCGGTAGTGTCGTAGGTCCTGTCGCCCCGCCGCCAGCAGAATCGCGTCCTTTAGTTGGCTGCCACCAGCATTCCTTACACCGCTCCTAGCCGGGAGGGTGGGGGTGATTGGATTCCCTTGGCCGAGCCTACTCAACTTAGCTACCCACTCTTCTTCCTCTATCTGAGTTATCCCCGAAAGGAGTAATGACCCGGGAGTGTGGAGGCTGTGCCAGGATCAGTTTGGCCATTAGGGCCGGCTGATGGCGTTGGTGCTGCTGCGAGCGGTGCGCCCCCGGAGAGAAGGTGGAGCCCTCAGAAACCTCAGGGGAAGGGGGAACTCCAGGATCCCTGACCCTTCTGCCAAGTAAAATCTCCCGTGGAAGTCCTCTTTTGGCATCACAGAGAGTCGGGAACCGGGAGCGGAAACCCTGAGCGGGCTCAGTTTCTTAAGACGTGGGCCATTTTTCTTGAACCTTCCCTTCTAGAATCCCGTGTGTCTGAGAGTGTTGTGCGTTGAGTGGTTCACTAAAGACCCTAGATTTGCCGGTTCGTGGGACTCACTAACTCTGTTTGCCCTTTCTGATGTCCGGATGTGTATATGGGGTAGAAAGGAAGTGAGCAAAGTGTGACAGGGAGTGGTATTGAGTCCCCTTTTTGTTCCGTGAAGCTTTCTCCAGCTCTTTGAGCTTCCGCTTCTCCGGGTTTGCTTCTTGTTGGTACAGCCGGGCCACATGCCTGGGTTATGGCCACTTTGAGGAGGTTTATAGCCAATTACAGCCGTATAAATCAGAGCGGCACTTGGGGGCCTGACTCTGGACACTTCTGCGTCACTGCACACACCCCGTCAGCGTCCTGGTGGGCAATGCTGTCGGGGAGAAGCCTACAGATTAGCCTCCAGTGGGCTTTGGCATTGTCGTTTCCAAGAAGACTTACTCCCAATCCTGTCCGAAGGAAAGAGAGCGCAGATCGCCGGTAGGGGTCTTAGACTGGCGAAAGAACTTTTGCGTTTAGGGGGTGGGTGGTCCGAGACTAGGGTCCTGGGAGGGGGAGGAGAACCTCAGGAGCCCAGGCCGCGAGGTCAGCAGATGAGAGGTCGCTGTGAAGTCCCGCGCCGAGGTGGCAAGGCCGCTGTCGGCGCCGGGCGCCCTTGTGATGTTAATGTAGGGAAGCTGTGGCCCGCAGTGCCGGAGCCCGACTCCTCTGCAGAGCGTCATCTGTCAAGGGGCAGAGGCGTGTACGCCGCCCGGCCGGCTTTGATGTACACCTTTTCAGCCCAGCCATTGTCTCTTTTAGGGCCCGGAAAGAGGGTGGTGACTTTCGCAGTCAATAATGAATTCTGACAACTCCTTCTCATCCCTCCCCTCTTCCAGCCCCCTTCCTTGGTTCCCAGGGGGTGCGGGGCGCCTGCAAGACCCTTGGGGAACGGACCGCAGAGCTCACGGAATCACCATCTTTGCGTTCCCCAGCCAGCGCGTGGTGCTCTCAAGGCAGCATCCATCCTAAGGCGAGGACCTAAGGCAGGCTTGGGGTTGGGGGGGGGGGGGCTGTTCTGCACCTCACTTCCCAGGTCTGATGGTCTCCTTTAGGATTACAAGCTCTTTGCTATTCGTTCTGCACATCCGGGATTAGGATCTGTCGTCTTCTGTGGAGTGGGGCACTCGCAAGTGGGGTACACGCGGTAGCTCCTGGACTGGTTTGGATCCCTTGACTTCCAAAGCAGGCGCGGGGTCGGGGCCGCAGCGCCCATTCAAATGCGCCTGCGGGGCTGTGTTTATGTTAATGCGCCTGGCGGGGAAGGGGATGAAAGCTGAGGCCGCCATTTGCTCAGTAGTGGTAATTCAAACAGAATGCGGTTGTTATTAAGGCATTGAAAGGGCTTTTCTTTGATAAGATCTCCTGTCTTGCATTGTTTGCGGCTGTGTTCCCCTTTCAGCGGCTGGGGGAGCTCTCTCTGATCCCTCCTGTATCTTCCCAGGGCGCTTTTGTTGTGGTTTGCATAGGTTTTTACCTGAACAAAGTCAGCCTGCGGGGCCTTAAACACCTCTGGGTAACTCCCACCCCTTAGATCTCCTTGTTCAACTAGGCACTGAGCGCCAAGACCTGTTCTGCTGTGAGATCTCTCAACTCGGGACGTGGAACAGTTCCTGGCCAGCATTCTGTCCAGAAGCAACCCCGACTAACCGGGTTGAATAGCCAGAGTCCAGCCTGGTCCAGCAGTCCTATTTGTCAAGGTCCTTCAGTAAAACAATCAATCCAAGATTTAATATGTTGACTCAATCCAATGATCACAGGTCACTTGGTCAGGATAGTGGCCGCAGGGGATAAATGGGGAATTAAAAAGAAAAAAGTGCCCTGGGCTAAACCTGGTTGGGCAGGTGTAAAGTGTTCTTACTAGGAGGGTTTTCCTCGTGACAATATGGAGCCTGGCTCAGAATTCCGGGGCAGGACTTATTGTGTCTAGGGGGGTGATGCTGGTGGCTGTTCTGGATCTGCTAGCCCCTGTATCCATCTTTCCACGGTATTGAATCAAAAGGTAACTACCAGTTTATCCTGACACCACATCCTAGGTATTTTCAAAGTGGTCTGCCATTTCTAGTAAGTCTGAGAATGTGGGTATTGATGTTTCTGGGGACTCTGGCCACTTTCCCCACCCCCGTTTCTTCTAATCCTAAATATACTAGATTTGGTTTATGGAAAGGAGGGGGCTGCGTGAGAGGTTTCCGTTTCCGCTTAGTTGTACCCCCAGACTTACACCCTCCCACTCCCCCCTCCCCAGGATCCTGCGGGTGGGTATTGTCAGCCTGGGTAGTAGCCGATCTCCTTCCCCCATCCGTAGATGAAGAGAAATGACTCCTGGGTTAGGGAGGTTTGTCATTACCTATGACTGATGGATTGTAGTTCTTAGCCAAAACTTCTCCTTCCTCCACAG
Seq C2 exon
TGAAAACCAGGACGAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAATTTCACTATAGTCGATACATCACCATCAGGAGGAAAGCTGAGTTGGCCGCCACACTCGGGCTCTCGGAGAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032759:ENSRNOT00000048188:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.592 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=WD(100=92.8)
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=85.7)
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:
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]