DreINT0044537 @ danRer10
Intron Retention
Gene
ENSDARG00000036292 | cdx4
Description
caudal type homeobox 4 [Source:ZFIN;Acc:ZDB-GENE-980526-330]
Coordinates
chr14:32622362-32624855:-
Coord C1 exon
chr14:32624220-32624855
Coord A exon
chr14:32622508-32624219
Coord C2 exon
chr14:32622362-32622507
Length
1712 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
TGACTTGGTTTTATTTTCAGGCA
3' ss Score
8.94
Exon sequences
Seq C1 exon
AGACTCACATCATGTTTGATTGAAGCACGTCAAGGACTACGTCGCGTGACCCGGAGCTCCTTTTGGACTATTACACTTCCAGATAAATAGTATTGAAGAAAAAGTTTTTGAGTCGGGCCTTGGATCCAAGTGATATTTGGCTTGATGCATGGCTGGCATGTTGCCTTAAAAAAAGTTATTTTAGGGGTTTCTTCCAAATCATGTACGTTGGATACCTTTTGGAGAAAGAGGCAAGCATGTATCACCAAGGAGCGGTTCGTCGATCTGGCATCAGTCTTCCACCACAGAACTTTGTTTCCACACCTCAGTATTCAGATTTTACAGGATACCATCATGTGCCCAATATGGAGACACACGCACAGTCGGCAGGGGCATGGGGCGCTCCTTATGGCGCTCCGAGAGAGGACTGGGGCGCCTACAGCCTCGGACCTCCAAATTCTATTTCTGCACCTATGAGCAATTCATCTCCGGGACCAGTTTCCTATTGCTCGCCCGATTATAACACCATGCACGGCCCTGGATCGGCGGTTCTTCCTCCACCACCTGAAAATATTCCTGTGGCCCAACTATCCCCAGAGAGAGAAAGGCGTAATTCCTATCAGTGGATGAGCAAAACCGTCCAGTCGTCATCAACCG
Seq A exon
GTAAGGCCAATAAATGTCTTTTCTGTAGCATAACAAGGCCTAAATGTCTGACAGACCGCAAAAAGGCGCAGCACAGTGGATAATTATGAAGTTACAACATGTAAATTGCGAAAATTGGAAGGTGTTGAAGTCAGTGATTGGAAAAATGAAAGTTCAAAATGACAGACATGTTTCCTTGCTATATATATATATATATATATATATATATATAATGACAAAAGTTTATATTATATATGAAGAGTTCAGATGCTAAAAACTCTAAATGCTGGAATTTTCCTCTGAGTATTTTTAGTGTATTCCAGTAAATATGTTGAGAAAAACGCTCCTTTTAGAAGGAAATTTCAGACAGCATTTAGAGGGTTAATCTAAATTTACTCTAATTGTATACCGAAAAAATTAAATAGTGTAATTAATGTAATAGTTTTTAAAATTTTGCTTTGATATTTTATATACACAAATTGTGCAAAATGCAACATGGGGAAAAATATTAACATTGTATCAGGCAGGCGTAATTGAACATCTGACAAAACTGCATGCCATTTTAAATAGTTTTACGCATGCCAAGCTTCACATAACATTTCTAATGCTCTCACTAATTCTGATATTTTTATATCAGTTTATTTCCCGAGAATGTTTGAAAAAAATCGCATGGGAAAATGCTTCACAAAATGAAGGTGTTGGGAATTGGCGCCAGGGTCACTTGTAATGCTAATTTGCGACTCCCGTAAACAAGATGTGAGGTCTACTTTCCTGTTACATTGTCTCAGGTTTTGAGGGTTATCTGTCATATTCAGGCGGCGACTTCTTTCAACACCTTTTTCACTTTGATATGCAGCAGCTCGTCTTCCTCTGTCTCTGTTCTTGAGGGTTATATTACCTCAAAGAGCGACAAATTTCACAGCATATAAATTTCTGCTGTCTCCGGCGCACAGACTAAAATATCTTAAAGAAAACAACTGCTTACAGAGTCACACGTCCTAACTGTAAAAGACAACTTTGAGTGTTCAGTTGTGCTTTTTTTAAAGTAATGTTTTGGAAATTAAACATTCAGTAAAACATTTGTAGTTTGCTTCATCAAGCTTTCACTGAGTTTGCCGCTAAACTTAATATTAAAACATTTATATTTATATAGTTTTATTTTCGAGGTTGGATGCATATCAAACAAGTGCAGCCTGCTCTTGGTTTGAGGAAAGGATTTTTGATGTTATCTCCTGGTAATTCTTTGTAGGACGTATGTTGTCTCTTAACACATCAATGGCATTTGGGTAAAGTCTTTGCATCTCTTTGTTCTGCAGTTTGTCAAAAAAATCTCAGCAAAGAAGATCAGAAGCTCAATTTGCATATCGGGAGATGTGATCTTGGTTTATAGTAGGCTGCTATTGACCGAATATTTAAGAGTTTTTATGAATTATAGCTAAAGAAGTTATTGGTACAGTTATTCTGAAATCAGCAGTGATTAATGATTCAATTGCTAATGCAACGATACATAATTATTTAATTGTGAATGCAACAATAAATGATTAGGTTAATTATATCAATTACATTATAGCCTATATAAATTATGGCATTGCAATTTTTTTTATTTGCTATGTTGCTTGGTGATTATTTTTTTGCTTATTCTTTCTGTCTCAGCAAGTATGGACTTATGTATGCCTTTCGCAACGATTTCTTCGTTTTGCGCAAATTTTTTCATGACTTGGTTTTATTTTCAG
Seq C2 exon
GCAAAACGAGAACGAAGGAGAAATACCGAGTGGTATACACAGATCACCAAAGGCTGGAGCTGGAGAAAGAGTTTCATTTTAATCGCTATATCACAATCAGAAGAAAATCCGAACTTGCTGTAAACCTCGGGCTTTCAGAGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036292:ENSDART00000114973:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.644 A=NA C2=0.286
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PU(98.5=91.1)
A:
NA
C2:
PF047317=Caudal_act=PD(0.7=2.0),PF0004624=Homeobox=PU(73.7=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCTCGGACCTCCAAATTC
R:
AAGCCCGAGGTTTACAGCAAG
Band lengths:
352-2064
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]