RnoINT0033697 @ rn6
Intron Retention
Gene
ENSRNOG00000060334 | Cdx1
Description
caudal type homeo box 1 [Source:RGD Symbol;Acc:621233]
Coordinates
chr18:56338336-56339185:-
Coord C1 exon
chr18:56339040-56339185
Coord A exon
chr18:56338567-56339039
Coord C2 exon
chr18:56338336-56338566
Length
473 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AATTCTCTGCAATCCCACAGGTA
3' ss Score
7.97
Exon sequences
Seq C1 exon
GTAAGACTCGGACCAAGGACAAGTACCGCGTGGTCTATACAGACCACCAACGTCTAGAGCTGGAAAAGGAGTTTCACTACAGTCGGTACATCACCATTCGGCGCAAGTCAGAGCTGGCTGCTAACTTGGGTCTCACAGAGCGGCAG
Seq A exon
GTATGTGGGCCCTCCAACTCAGCTCAAGTAGTTGGGCTTTCAGGTTGCCATGCATGGACAGAGCCCACAAAAAAAAATAAAAAAAAGGTAGTCTCCAGACTACTGGCACAAAACCACACACTGAACCACTGCCATACCACCAACTAAACCCAACATTATTCCATACACACAAACAGACATATGTATGTGTGCGCACACACACACACACACACACACACACACACACACACACACACACACAGAGGCTACAGTGGCTGGTGATCAATGCTATTCAAACCCAGAGGATGGGCAGTCACAGAACATGGGGGCTCTGGAGGACTGGGGCCTTGTAGGAGGTTTCAGAGAAGGGTGTCTAGAGCACAGGGAGAATGTATTTTAGTGGTGACTGGAGCAGAAAGTGGATCATGAAGACCACCTCTCCCAGCCCAGCTCCTTCCTAAAATCTGCAGCATAAATTCTCTGCAATCCCACAG
Seq C2 exon
GTAAAGATCTGGTTCCAGAACCGTCGGGCCAAGGAGCGTAAAGTAAACAAGAAGAAACAGCAGCAGCAGCAGCAGCAACAGCAGCAGCCCATGCCTCCCACACAGTTGCCCCTGCCCCTGGATGGCACCCCCACACCATCGGGGCCACCCCTGGGGAGTCTATGCCCCACCAATGCTGGTCTTCTGGGCACCCCCTCCCCAGTGCCGGTCAAGGAGGAGTTTTTACCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000060334:ENSRNOT00000083379:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.947
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7),PF119313=DUF3449=PU(44.8=79.6)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=16.9),PF119313=DUF3449=PD(52.9=59.7)
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:
CAAGGACAAGTACCGCGTGG
R:
AAAAACTCCTCCTTGACCGGC
Band lengths:
357-830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]