DreINT0036770 @ danRer10
Intron Retention
Gene
ENSDARG00000019013 | barhl1b
Description
BarH-like homeobox 1b [Source:ZFIN;Acc:ZDB-GENE-060118-2]
Coordinates
chr21:17443394-17445829:-
Coord C1 exon
chr21:17445237-17445829
Coord A exon
chr21:17443617-17445236
Coord C2 exon
chr21:17443394-17443616
Length
1620 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GTGCCCTTGTGTTGTTTTAGTAA
3' ss Score
7.76
Exon sequences
Seq C1 exon
TGAATATTTCTCATTTCCGATTCTGCTTTGGATTTTCCTCCTGGATAGACCGCTATTAAATCGAGCGCCATTCACGCAGAACTTGGTTGAATACAGATGATAATCTGAACAGAGGCTTCACGCAAGCAGCAGTGTGGAGATGGAAGCGTCCACCAACGGCTCCAGTTTTGGAATCGACTCCCTGCTGTCCCACAGGCCCGGAAGCCCAGTCATCTCGAAAGGGGACAGTTTGGTTGGGGAATGCCGGTCCCCGCTGGAGTTCAGTCCCAGGTCAGACTTAGAGAGCGGTTGTTCTTCTCCTCCGTCCCCGAGGCGGGAGTGCGTTGAGGATGCGGCGCAGAGACAGGGTCACCCGCTCGCTTACGCGTCCCATTTGCAACACGGGCCGATCTCCGCTGGATCGCAACCTCGGACTGTCACTTCATCCTTTTTAATAAGAGACATTCTTGCTGACTGTAAACCTTTAGCGGCGTGCGCTCCTTATTCCAGCAACGGCCAGCCGACACAGGAGGCAGGGAGACTGGCATCTAAAATCGCAGACGACTTAATAGAAAAGATCCACAGTAACTCATCGTCAGACAGTGAATACAAAG
Seq A exon
GTAAAAATGCAAACTCGTTTTTAAGAGGCATTTTAAAATTATTTCACGGGAACTATAATTTGCCGTTTGCATTTTACAGTGTCCAGTCATGCCTTTGCTGACATTGGCTATATTGCTAAAAGAACTGGGGTTAGAAATTAAACGTACATGTAAAATTACAATGATTCTGTTACAATGGAATTTTCGTAATTGCACACTTTACTGTTTGTTTACTACTTTTGAATGGCCACTGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAAAAACAAAGCATATTTATATTATAGTCAACATTTTACAAGTATCTCGTATTTTTGATAATAAATATAAGATAAATGAATTTCTCTTAAATGCATTAATAGGGATTTTTTTGTTTACAGTGCATAAATTATTACACGACATATAAGACGTATTGTATATTTTATTTTGCTTTTTAAAATAAAAGCAAATTATAAAGTAAAATACGTCAAATGTGCCTTGTTTATTGTTAAATCATGCAGAACGAATGTTGAAAAAGAAAAAAAGCAACACAATTCTTTAGGGATTTCTTCATGTTAAATTAAATCTGGAAAAACATTTCTTTCTGCGACAGACCATTTCTTATTATTATCAGACCATTATTACTTAATATTAAGTATGTCAAGATGCGAATCATACATAACAATTTAATATTGAAAATGTAGAAAAGATAATTAATCAGAAAATCAATTGCTTATTGTCGTTATTACTGTCACAAAAAATAAAAAAAATAAAAATAAATAAATACATGTAGCCTACATGTTTATTTATATTTTTGTGGTAATGTTGGTGTGTGTATTTGGCCTAGGCTGAAGATGGCATTGTAGTTGTTGATTGCTAATTTGTTCAAAATGTTATCATCACAATCTTAGTGGAAGTAGGGCATGATGGGTCACGTGTATTCGCCAATAGACCTTCAGCAAGAAATCTAAATATATTTCTTCTCTCCCATCATAACATTATTAGCTTGGCAACTCTATAGGCGCGGTGATCAAAATTAATGCTCTCCAAATCAAAGCCATTCCATCTCCAGAGCGCTTGTAAAGAGTGTGTGCGCCGCTTTGATTTTTTTTGCCTTTCTAGCCTCTTATATTTCGGGGATTTGATGCAATTTGTCCCAGTGCTAATCAGATTTGTACCGCACGAGGTCGGTCCGCTCTTTATTTCGCTCTTATCCCCGGCCCTGTGAAGTTTCTCCGGTCTCGGTTGAAAGGTTTCCATCCCTTGTGGCTCAATTAGCCGGATTATTGTGCTCCTTGAGAGACGACTCAACTACTCGACTGGCAAGGTCTCTCGCGTCGTGTCCCTCTCTTTCTGGGTTCAGAGAGAAAAGAGTTTGGTTTAGAGAGAGGTTGAATTAAATATCACAAATTCTGAGGAGAAAAAAAAACATTATAGAGGCCATCAAGAGTGTGGAAACCTTTGACGCCATAACATGACTTGTCAAAATGGGGTGCATGCATGTGCTGAAATACACAGGCTAACTAACTCGTGCTAAAATGGCCTAATCAGTGCCCTTGTGTTGTTTTAG
Seq C2 exon
TAAAAGAGGAGGGCGACAGGGAGATCTCGAGCAGCAGAGACAGCCCGCAGGTTCGCCTGAAGAAGCCACGGAAAGCGCGGACCGCCTTCACTGACCATCAGCTCGCCCAGCTGGAGCGCAGTTTTGAGCGTCAGAAGTACCTGAGCGTGCAGGACAGGATGGAGCTGGCAGCATCTCTCAACCTGACCGACACGCAGGTCAAAACCTGGTACCAGAACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019013:ENSDART00000004548:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.625 A=NA C2=0.400
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(89.5=68.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACCTCGGACTGTCACTTC
R:
CTGCACGCTCAGGTACTTCTG
Band lengths:
343-1963
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]