DreINT0078831 @ danRer10
Intron Retention
Gene
ENSDARG00000054030 | hoxb5b
Description
homeobox B5b [Source:ZFIN;Acc:ZDB-GENE-000823-6]
Coordinates
chr12:27038299-27040375:+
Coord C1 exon
chr12:27038299-27038978
Coord A exon
chr12:27038979-27039429
Coord C2 exon
chr12:27039430-27040375
Length
451 bp
Sequences
Splice sites
5' ss Seq
ATGGTATAA
5' ss Score
2.05
3' ss Seq
TTTGCCCTTGCTTATGCCAGATA
3' ss Score
7.14
Exon sequences
Seq C1 exon
ACAGTGCATTGCTATAATTCATTATTACATCATAAATTGTGCGGCGCTGGATTTTAACGACCAAGATCTACAAATCAAGACATTTTAAAACATCCAAATGAGCTCTTATTTTCTAAACTCGTTCTCAGGGCGCTATCCGAATGGGTCTGACTATCAGTTACTAAATTATGGTACTAACGGCGCTATGAACGCTTCTTACAGGGACTCCACCAGCATGCATTCCGGGTCTTTCGGTTACAACTACAATGGAATAGACCTCAGTGTAAACCGTCCCAACAATGGCCATTTCGGGGCAGTTGGAGATAATTCTCGCGCTTTCCAAAATCCGAGTCAGGAGACCCGGTACAGACAGTCGAGCTGCTCTCTCTCGTCTCCAGATCCTCTGTCTTGTGCCACCAGCGATACTCTGGAATTGAAGGGTTCCTCTCCTCCATCTGATCAGAGCACACCAACCGGCAACAGCAGACTTACCAACAGCAACAATCTTACCAGCAGCAATAGCACACATTTTGCGGACACAGATGAAACCAATGTCTCGTCCGAGACCGAGGAAGGAGCACAGACCACCACCACCAGTCGTACGCAGAAGCAAGAATCTGTGGCGACCTCGACTACAACACCTAACGACGGTCAAACTCCACAGATATTCCCCTGGATGAGGAAGCTGCACATTAGCCATG
Seq A exon
GTATAAACATCTCTGTATTTTTTTTATTTGGACATGATCAAATGAAAATACAACAGTCCTATCTTAATGATTAGTCTTTTTTTTATTTTAATTTATTTACAGCTTACACGTGGATTAAATGCATGTTTTTCAATTCAGATTTTATTTTAAGTAGTAGTATTCAATTAGCAACCTTCTAATGTTTGTCTTAAAAATTAAAGCTTAAACGGACCATTGAGTTAGCATAAGTATAGGTTAAATAGAGAATAACTACTCTCTGAGAGGCGACTGCATGGTAAATTATTGTGCATCAGTAAAGTCATAAAATGCAATGGTTATAAACCACACATCTTTTTGAATATACATATGAACCAGTAGTCCAACATCCAAAATGTAATGGACGCTTAAGTCCATTTGCGTTTAATGGCTTTGTGATATTTACTTGTTATCTTTTTGCCCTTGCTTATGCCAG
Seq C2 exon
ATATGACTGGACCTGATGGAAAACGGGCTCGAACAGCTTACACTCGCTACCAGACGCTCGAGCTGGAGAAAGAGTTCCATTTCAATAGATATCTGACGCGCAGGAGGAGAATAGAGATAGCTCACGCTCTCTGCCTCTCAGAGAGGCAAATCAAAATCTGGTTCCAAAATCGCAGGATGAAATGGAAGAAGGACAATAAACTGAAAAGTATGAGTCTCGCTACAGCGGGGAGCGCGTTTCAAAATTGATCAAATCACATCACATCAATTGGAAAATTCGACTACTGTTACAGCGCTGCACCTTCAGCTTGTTCTCACCTGACGACGTGTGATTCTCCCGTGCAACTCAAAATTGTCAGCTGTTGAATGTTATCATATGCTAAACTAGTTACAATTGCCATAAAATGAGTGTGAATGTCAAGTGTGTCAAGTTTATACATTCGTGGAGGAAAGCATGTTCCATGTGAGCTATTCGTGCAACGTATTAGATCTACAAAAATTATGTACAGTACAACTCGCACTACCTAACTATCTTAAGTGATAGTGTAAAAAGAGAATCTTTTGTTGTATCCTTGAACTTGTATTGAAACGTCATGTATTATTCAAGCAACATGCTATATTCTTGTTATGTGCTGGGCTTTTTTGATTTCTCGTCTGATACCTGCATCGCGAGGAAATGAATCTTTTCGCACTTACATTTGTGTACTTAGGCTGCAGCACAAAATTACTTTGGGCTCGTAAGATGTCCTATGAAGAATGTCTTTATACAGTAGTGACCAATATGTTATTTGTAGTGCACAACGTGAGTTATGGACGTTCTGTGTTAAAAGTTGGATAAAAAATGTTTTGTCATCGACACGTTATTGGTATCTCTGCCATTTTTTGTATTTGTGTCTAAAATGAAAACGAGTTCATCCAAAAAGAATAATAAAGTTTTCTTTCTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000054030:ENSDART00000076161:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.759 A=NA C2=0.183
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=68.7)
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:
AACGACGGTCAAACTCCACAG
R:
GTGCAGCGCTGTAACAGTAGT
Band lengths:
358-809
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]