DreINT0044536 @ danRer10
Intron Retention
Gene
ENSDARG00000058999 | cdx1b
Description
caudal type homeobox 1 b [Source:ZFIN;Acc:ZDB-GENE-070615-29]
Coordinates
chr21:43984306-43987278:-
Coord C1 exon
chr21:43987130-43987278
Coord A exon
chr21:43985603-43987129
Coord C2 exon
chr21:43984306-43985602
Length
1527 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TGGCATGTTGTTGTTGACAGGTG
3' ss Score
8.36
Exon sequences
Seq C1 exon
GAGGGAAGACCAGAACAAAAGACAAATACCGGGTGGTGTACACAGATCATCAGCGTCTGGAGCTGGAGAAAGAGTTTCATTACAGCCGCTACATCACAATAAGAAGAAAAGCAGAACTGGCAACCGCACTCAGTCTGTCAGAGAGACAG
Seq A exon
GTCAGCTGCTTTTATACTGTTCTTAACGCCACAATTCACGAAAAATGAAAATTCTGTGCTTATTTACTCACTCTTCACTTGTTTAAATAGTCACATTAATTAAAATTATACTTTAGTGACAAGGCAGCCCTGGCCCAATCAGGTCAGTAACAATCCTGTCTACTATCCCGAGCATCTCTCACGCTTGCCCCAGGCCAATGGGCAGTCCTTATTGTTGTTATTGTTACTATGTACAGAAAGCCTTCTTGGCTAAACAACAGGGATCCAACATTCTGCGAACCAAAAAAAAAATGTTCCCAATATGTTCAGTGTTAGCTGGTATACAAAGTTCTTTTTAGTACTTTGAGGGCATAAAGAAACTCGAAAAGTCTGAGTGACCTTATCCTATATTCGACCCTTTCCACATCTCCTCACTGCAGTGGGCTGGGTTGTAAATGTGTCGCACTGCTTGAGTGTATTGATAAACACAACATTAATGGCGACTGAGCAGTTTCCGATTGTGTAATTGTCATGAACAAATAGCAGCTCAAAGGTGTTTGGGAACAAAACAAACCTTCTCAAAAAGTCATTGGTAGGCTGTTTAGAACTGCCAATGTTTAACTTAATTTGTTTGTTTAAATTCAGCCCATTTATTTGCAATTGTTATTTCCGATTGTTTGCAGCCACTTACCTTAAAAATAATTGTAAATCCAATGAACCATTGTTTTTAGCACAGCGTTTTGAAAACAGACATCACTATCATCACCTTTAGCACAAAAAATATGTATGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTAGCAGTGTGATATGGCTGTATGTCGGTGGGAGGCGTGCGTTGGCACGAGACCACAGGCCGAGAGCCTTAGTGCTCCCACCAGTGCCGATATACAGCCATATCGCACTAGTACGAGTGTGATATTGCATTTAAACAACATTGTGACGGCCTAATTGTGTATGTAAACACAAAATCAAACATGGAGAGTCTCAAAAACCCTTTTGTATGAGGAACTACTTTCTTCCGCGTTGTATTCAAATCATAAGCTGACAGTTAAACAGCTGAGCGTGCATCTTTTAAACTTTAGATCTGGAGTGTCTGCTTTTTGCTGGCTGTATGTGGGCGGAGTTATACACAAAGGGTAAAGAGGCTGTATGGGTGCTGATATTACTTAATTATATCACGGCTATCAGCCAATCAGATTCGAGAACCAGACAGAACTGTTGTATATATATATATATATAGGCAATATGACTAATGGCATGTTGTTGTTGACAG
Seq C2 exon
GTGAAGATCTGGTTCCAGAACCGCCGTGCTAAAGAGAGGAAAATCAATAAGAAGAAAATGCAGCAGCCTCAGCCGGCATCCACCACCACACCCACCCCACCGGGCTCAGCACTACCAGGCAATGTGCCGATGGTGACCAGCAGCAGTAGCGGTGGCCTCGTGTCCCCGCCCATGCCAATGTCCATCAAAGAAGAGTATTGAGGACTCGGAAAACCTGGACTGATAGAGATTTTTATATCGAAACACACTAATCCAACACAGGGTACTCTTCATGAAATCAGCACATCTTTCCTGGAGCACTGAAAATAATGTTGTTGCAAACGATTTATGTGGGCTGAAGTTAAACAAACAAAAATGAGTTGAGTAGTGTTCAGCTTAATTTGTTTGTTTAAATTTAGCCCAAATAAAGTATTTGCAACCACACGCCTTAAAAGAATTCATCCAGCAGGCACAGGACGTCAACATGACCTCAGACTGACGTTGTAGGTCAACATCATGGGGACGTTGCAAGTTGTTTGGAATGAAAATCAAGTGGACATGAGAACCCAATGTCAGGCTGATGTTTACGTCCAACCAAAAATCAACCAATTATCAACGTCTAATGATGTTGTGTGGATGTTGCCATTATGACGTCTATCAGATGTTGGATTTTGGTTGCCATTCCTGATGTATAAATGTCAGTATTTGGCGTCAATATTATGTTGGTTTAAAATGTTGGCAAAAAGAAAACGTAAAATCAACCAAATTTCAACGTCTAATGATGTTACAGCTTGACGTTGTGTGGATGTTACCACTATGACATCTATTAGATGTTGGATTTCGATAGCCATAAATGATGTATTTGACATAAATAAGACGTTGGTTTAAGATGTTTGCTTAACATTGCGTTTTGGTTACTCTCCAACACAACCTAAAATCAACCAAATATCATATCACATATACAATATGTGGATGTTACCATTATGACGACTATCAGACGTTGGACTTTGGTTGCCATACCTGATGACGTTGGACTGTCCAACACAACCTAATATCAACCAAATATCAATGTCATTCGTTGTCATTATTGGACATCAAAATAACGTTGTCCTTAGACGCTGAGTAGACATTGAATTTTGGTCACCTGACGTCACAACCTAAATCTAACCTAATATTAACATCTTATGACATCGTTTGCCTGCTCTGTAGTAAATCCAATGACTCACTTTTTTTCAGCAAAATGAAATTTTATGGAATTTTCTTGACAAATACAAATAGTCGACAGCCACACTTCTAAAAATAAAGGTTCTTAGACGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058999:ENSDART00000081993:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.864
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(0.8=2.0),PF0004624=Homeobox=PU(73.7=84.0)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=19.4)
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:
GAAAAGCAGAACTGGCAACCG
R:
GTGCTCCAGGAAAGATGTGCT
Band lengths:
344-1871
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]