DreINT0044538 @ danRer10
Intron Retention
Gene
ENSDARG00000036292 | cdx4
Description
caudal type homeobox 4 [Source:ZFIN;Acc:ZDB-GENE-980526-330]
Coordinates
chr14:32621404-32622507:-
Coord C1 exon
chr14:32622362-32622507
Coord A exon
chr14:32622260-32622361
Coord C2 exon
chr14:32621404-32622259
Length
102 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TTATCTTGTCCCCCTTACAGGTT
3' ss Score
12.17
Exon sequences
Seq C1 exon
GCAAAACGAGAACGAAGGAGAAATACCGAGTGGTATACACAGATCACCAAAGGCTGGAGCTGGAGAAAGAGTTTCATTTTAATCGCTATATCACAATCAGAAGAAAATCCGAACTTGCTGTAAACCTCGGGCTTTCAGAGAGACAG
Seq A exon
GTAAATATATCTTTTTCATTCATATTTTTACTTTTCAAATAATCTCACTTGTTGAAAACATAAATGTTGGTTCTCTAATGCTTTATCTTGTCCCCCTTACAG
Seq C2 exon
GTTAAGATCTGGTTTCAGAACCGCAGAGCTAAGGAAAGGAAATTAATCAAAAAGAAATTGGGTCAGTCTGACGGAAGCGGAGGGTCAGTGCACAGCGACCCAGGCTCCGTCAGTCCTCTACCGGTACCAGGGTCACTGAGTCCTTCAGATATACACGGTTCTCTGTATCCAGCACAAATGAACGCCTTGCCGTCCATGAGGAACATACAGCAAGTTACTGTCACTCAGTGAACTCGAACTTGGAACATCCAACTTTAACTGAGCACTCCAACACGCTGAAAGGACAGAACCAAACGTGGTCAAAAAGGATTACAAACTATTAATGAATAAATGAATGAATAAATAAATAAGAGGCGTGGGTTGTGGATTACAACCGAAGAATCACGTCTGAAATGCGACGAAATGCTGGAGGCTCTTCAAATATTGTTTTAATAGAATAGTTTTTAAAATTAAGAAAAAAAACTACAAAAACCTTGTTCGTCTGATCCAGAGACTAAATATTTTAATGGTTTGTGTTTTCTCGAATAAGATATAAATATCTTTTTTCTGTATGTGGTGAGTGTATCTAAATGTTTGTTTGTATATAAAATGAGAACTACAGGTACGGAGTTTCATGGGACGTGTAATGATCCTTACCCTGGAACTGTTAAACTTTTATTGTCTGTGAAAACCAATGACCTGCGATGTCAGGCTGTTTTATGCGCCAGTTTGTGTCCAAAGCGCACGTCGTTCACTTTCTTTTCACAGGGGTGATGTGCAGGTGTCACATACCAGATACGGGTATAACGTTTGATTTCAGCAATGTGTAAATAAATGTTTTGCAATAACTTTTATTGTGTCTTCATGTATCATTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036292:ENSDART00000114973:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(0.7=2.0),PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=16.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGCTGGAGCTGGAGAAAGA
R:
TGAAGGACTCAGTGACCCTGG
Band lengths:
244-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]