DreINT0078832 @ danRer10
Intron Retention
Gene
ENSDARG00000026513 | hoxb6b
Description
homeobox B6b [Source:ZFIN;Acc:ZDB-GENE-000823-7]
Coordinates
chr12:27035779-27037408:+
Coord C1 exon
chr12:27035779-27036244
Coord A exon
chr12:27036245-27036680
Coord C2 exon
chr12:27036681-27037408
Length
436 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TCTTTCACTTTTCCTGACAGGAA
3' ss Score
10.98
Exon sequences
Seq C1 exon
AAACACAACAAATCATAACACACGGACAATAACACTGGCCACCCCATGAGTTCCTATTTCGTCAACTCAACTTTTCCCGTGTCTCTACCCGGAGGACAGGAGTCTTTCTTGGGTCAGATACCGCTATATTCCTCTGGATATACAGATTCTTTAAGACATTATCCAAGCGCTACGTTCGGAGCTACCAATGTCCAAGACAAGGTTTACACCTCCTCGTATTATCAGCAAGCTGGGGGTGTTTTTGGGAGAAGCGGATCCACCAGTGCTTGTGACTACTCAACACCCAATATTTACCGATCCGCTGACCGCTCGTGCGCTATTGGAAGTCTGGAAGACTCGCTGGTCCTAACCCAGGACCAGTGCAAGACGGACTGCACAGAACAGGGCACAGAGAGATATTTTAGCACTGAAGATAAACCATGTACCCCGGTTTACCCGTGGATGCAGAGGATGAACTCATGTAATG
Seq A exon
GTAAGACACATTCGTGATTTCCTTGCATGTCTTAGAAAAAGATAAGCAATTTTCTTTAGCCTACTTAGCACTACGAGACTGTCAACGAATAAAAACATAGCCTACATAATAAAGAGACATGGTCTACAGTGCTTAGAAAAAGTTTTTTATTAAGTAATTTATTTTATTTACTAAATAAAGAATAGCGGTTTAGGTAACACGATGCGTAAATATGTGTACAATACACCTAACTATGTCATAATCGTTATATAAAAATGCACGTCTTATCTGTAGATGCAGAGTGCAGATGTGAAATCTGATGTCACTGTATTAATTATAATCAACGTGATAATGATAATAGGGACAATTAGTTGCCAAGTGGTGTATTTATGTTGTACTGTTTGTATGTCTAGGCTATTGGATGTTGACCTAGAATGTCTTTCACTTTTCCTGACAG
Seq C2 exon
GAATGCCTGGCAGCACTGGCCGCAGGGGTCGTCAAACCTACACTCGGTTTCAGACTCTTGAACTGGAAAAGGAGTTCCACTTTAACAGATATTTGACAAGAAGGCGAAGAATTGAAATATCGCACGCTCTGTGTTTGACGGAACGACAGATCAAGATATGGTTCCAAAACCGCAGAATGAAATGGAAAAAGGAGAATAAAGCAGTGAACTCGGCAAAGGTCAGCGATGAGGAAGATGGTGGAAAGGCTGGATAAATGCTAAAAAACAGCTTATGACGAAGCCCTAGAAACACTGTACATAACATGTAGAATGTAGTTTTAATTAATACATACATGTTCTTTCCAACAAGAAAAAAAACTACCTAATAAGTGTTATGTCGACTCCAAAATGCTTCAAGAGAGATTTCTTTCTTATAAAAACAGGCATCGAACTCACCTCTGTAATGAAGGTAAAAGTTCTGGAAGGTGCTTTAACTACTGTTAAGTATTTTATTTGGACTTTCAAATGTAATAAGATGAACGTTTTCAAACGCTTAAGCGTTGTAATGCCTAATTTGAAAGAAAAGTTCATGCTTAAAACTTTGGGTTTAATGGTCCTGTATTCAGTCCACGTGTGTTAGAAAAAAGAAAATGTGACATTTTTATTCTTAATTTATTGGGTCGTCACTTTTGTGTAAATGTGAATGCACTATGAATAATACGCTACCATACTTTGTTAGCAATGTCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026513:ENSDART00000025966:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.381
Domain overlap (PFAM):
C1:
PF0038714=PI-PLC-Y=PU(60.6=40.4)
A:
NA
C2:
PF0038714=PI-PLC-Y=PD(38.3=42.4),PF0004624=Homeobox=WD(100=67.1)
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:
TAACCCAGGACCAGTGCAAGA
R:
TTCCTCATCGCTGACCTTTGC
Band lengths:
353-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]