DreINT0078835 @ danRer10
Intron Retention
Gene
ENSDARG00000054025 | hoxb8b
Description
homeobox B8b [Source:ZFIN;Acc:ZDB-GENE-980526-291]
Coordinates
chr12:27026249-27028811:+
Coord C1 exon
chr12:27026249-27026879
Coord A exon
chr12:27026880-27028353
Coord C2 exon
chr12:27028354-27028811
Length
1474 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CGCTTCTATTTCCCCCTTAGCTA
3' ss Score
7.39
Exon sequences
Seq C1 exon
CGGGGACCGTCACTAAGGAGTCATGTGGGTGCAGCTACGGATACATTTGTTTGCATGAATATTTACGACATTTTACGCATATAATTTCCACCTGGATGAATTCGTTTTTATTGCAATAGCAGGCCTCAAGCAACATAATTTATCTAGAGATTTCTTTATCTCAACACTGATTGCCAAAGTTTCACCGGGGAGTTGATCTTTCAAGCAATGAGTTCCTACTTCGTCAATTCCCTCTTCACTAAATTTAAAGGAGGCGATTCTCTGCGCTCCAACTACTATGACTGCCCAAGCTACACGCCGGATCTTGGAGGCAGACCATCTGTGCTGTACGGTCACAACACAGGATCTGCGTTTCAGCACGCGGCTCAGTTCCCGGATTTCTACCACCACGGTACATCATCATTCCCCCACGCGTCTTACCAGCAGACCCCGTGCGCAGTTGCGTACCCTGGAGATGCCACGGGAAACATCTTGGGCCAGGACGGTTTACAGAAACAGTCGTTCTTTGGCGCGCCAGATTCGGATTTTACGCAGTTTGGGGATTGTAATTTAAAGGTCAGCGGTATCAGGGATGATCTGGAGAGTGCAGAACCGTGCACAGCGCAACTCTTCCCATGGATGAGACCACAAG
Seq A exon
GTGAGATGAGTGAAGAGAAACACCTAGTCTGTTATAGTCCCATATAAAACACTGCAGACAATGCTAGGCCTCTTATTACCCCCAATTAAACGCTTTATGGCACCTATAGATTACTAAGGAATTAACACCTTTTAAGAATATCCGGATTACGTGTGTACACATTGTGTTATGACAGTTAATAGAAGCTGTGAGGTTTTTTGACACTTCGTTACTTTATTAACAGATAGCCTAGATATATATGCCTATCCACCTTATTTCACAACATGTGTTTTTTATTTAAATACGCAGACTTCGTTATAACCACTCTTAATTTGTTTGACATTAATAGTATTAATGGTTCTAAAAACAATCATGCACTCAAAAATTATATTTGCTGTTTGTTTAAGCTACTTATTTAAAATGAACTAGAACAACACAGTTCTTATACTTACGTTTGGGGGGGGGGGGCAATTTGTTTGCTTTATGTTCAATCAACTTAAAAACTAATACATTGACCTAATTCCTTCATATTGTCCCAACACAAACCGATTGTGTGGAACCCAGCATCTTACAGCGTAAACAAGCACGAAATACTTGCATTTAAAAACATAGTTATTACTCTTAATAATAAAGATAGTTGAGTGTCATTGATTGTTCCAACTAGCGCCTTAAACATTTTTATTGCTCAAAATAATCTTTAGATTATTAAAGTGTTCCCCAAACTATGAAAACATAATATTTTTTGTGAACCCAATATTTAATAATAGTTTCTCATTGGCATCGATAGTTTCAAAATTTACTCACTAATTAAATATTTCCGTTTGCACAAAATTGTCTTTCAAATGTCAATGTTATTCACACACCGTAAAAAATCCAGGGTTCCATACAATTTATTCATGTTGTCCCAACACAAATCGATTAAGTTCACTTAACATTTTTAACAAATTTATGTAGATTGAACTTAAAAAATTAAGTTGTCTCAATGAAATCTCAAGAAGTGTTGTTTCAGCTCATTTTAAATAAGTAGACCGAACAAGTAAAAAATATTTTTTGAGTGCACTAAAAAAGTTTCTTAAGGAGAGCTCTTAAAAATTAAGATACTTATTAGTGTAAATAACTAATAATTTTAATAACTAATAAATAACTATTAAATATGTAATAATCTTAAAAAATATTTAAAGAACCATAAGTGCAAATAAGGTATCTTTATTTTTAAGAAAATAGCTTTATTGTTCTTTATGTTTGCTGATCACTGGAAAATACTCCAAGGAACACATAAAAGGTTCTTCTATGCCATCCATACTAAACCCCCGTTTTAAACTTTTATTTTAGGACATGGTACAGCATAACGCACTATTTACGTGCAGGTGAAATATCTGGTGAATGACACAGGATTAAAGTTACTTATAACCGCTCTCACGTTAAAACTATACGATAAGTATCTTAATCAAAAAGGCTTTCACCAGTATTAATGACGCTTCTATTTCCCCCTTAG
Seq C2 exon
CTACCGGACGGAGGAGGGGCAGGCAGACCTACAGCCGCTACCAGACGTTGGAGCTGGAGAAGGAGTTCCTATTCAATCCTTACCTGACCCGTAAGCGGCGCATCGAAGTGTCTCACGCACTGGCCCTCACTGAGAGGCAGGTAAAGATCTGGTTCCAGAACAGGCGTATGAAGTGGAAAAAAGAACACAACAAAGACAAGTTTCCCAGCAGCAAAGCAGAACAAGAAGAAATTGAGAGAGAGAGGCAAGAGGGGAGCCAGGTGTCAGAAAAACACACATCTGGAGAAGAGGACTCGGAGGCATCTAGCAATTCTAAATAGTCTTTTGACTATAAAAACATCACAATCGATCAACTTCAATTAAATAAAAGTCTGAAGTTCAAAAACGTTCGTCGACATGCAAAGGCTGTTGCATCATGTATTCAATTTATTGCAAACTTATGAGGCATTTATGTTTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000054025:ENSDART00000076154:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.028 A=NA C2=0.509
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=53.3)
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:
ATCTGGAGAGTGCAGAACCGT
R:
CCTCCGAGTCCTCTTCTCCAG
Band lengths:
357-1831
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]