DreINT0036771 @ danRer10
Intron Retention
Gene
ENSDARG00000019013 | barhl1b
Description
BarH-like homeobox 1b [Source:ZFIN;Acc:ZDB-GENE-060118-2]
Coordinates
chr21:17442058-17443616:-
Coord C1 exon
chr21:17443394-17443616
Coord A exon
chr21:17442388-17443393
Coord C2 exon
chr21:17442058-17442387
Length
1006 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
GTTTCTCCCTGGGAAAAAAGGAC
3' ss Score
-1.19
Exon sequences
Seq C1 exon
TAAAAGAGGAGGGCGACAGGGAGATCTCGAGCAGCAGAGACAGCCCGCAGGTTCGCCTGAAGAAGCCACGGAAAGCGCGGACCGCCTTCACTGACCATCAGCTCGCCCAGCTGGAGCGCAGTTTTGAGCGTCAGAAGTACCTGAGCGTGCAGGACAGGATGGAGCTGGCAGCATCTCTCAACCTGACCGACACGCAGGTCAAAACCTGGTACCAGAACAGGAG
Seq A exon
GTGAGCATGTGGTCAACTGGAAACGCATTTGTGTACATCCCATGCATTATTAAACATGCTGCAGAAATTTAATGGTAAATATTTTGGTGTTAAATTAATTTTCTAAATTGATATTCGTTTTATTTGGAAAAAAATGTACTTCATCAGTGTATTCAAATGTTTATTTATATATAGGCCTACAGTGTATTTTCTCTTTGATTTAGTATTCTCCTGCCAAACACAATAAAACACGTCAAATGACGTTGCTGCGTCACTTTTGATTTAATAAAAAGAAGGAAATGCTGCAGAGTAAATACTATTATTAATATAGCAAAAAATATTAGGAGCTAATAAATATATTTTACACAGCTTTCAAATTGATTTAAAAAAACATGGAAAAATTTATTTGAAAGATATTTTGTAAATATCACGAAAATCATTGCAGATAAAAGCAAAACATTACTCATGTTATATGTTTTATTGTTATTCTACACGTGGTTTCATGGCTTATTTTTATACTCCTGTAATTATGTGCCAAATTAAAAGATTTGAAATGAATATACAACATTTAATCCATTCTTTAATTATTCAACGTTTTAATGACGCGGGCAATCCTTGAATTGCTGAATTAGTTGTTTAATGTTAAAATACACGTTAAAATAACTCTCAGCACATTCATTTAAGTTAGTCACTTTTATTAGCCTTTTAGGTGTAAAATTTAGTTTTTCTGTTTTGTTCTTTTAACCCTTAATGATAATCATGTTATTACTGAATTGTGACGTTAAATGTAACATTAATGCTGATACCTGGAAACTGGAGATAAATCATTGATTTGTCAGTTTTTTTAAGGAAACTCTGGGTTTCATTTTTCTCTTGCGAATTGTCGTGCAATAATAAGCATTTTCCACTATTTTCTTTTTGTTATGTGCAGCTTTTATGACTTAGTAGATAAACTGCTGATTGCTAAATCATTTACATTTAATTATCTTTTGTACTAACAACATCCTGTTTCTCCCTGGGAAAAAAG
Seq C2 exon
GACTAAGTGGAAGAGGCAAACGGCGGTCGGACTGGAATTGTTAGCGGAGGCTGGAAATTACTCTGCGCTGCAAAGGATGTTCCCTTCGCCGTATTTCTACCCTCAAAGCCTGGTGTCGAATCTGGACCCTGGAGCAGCGCTCTACTTATACAGGGGACCTTCGGCGCCCCCGCCGGCGCTGCAGCGTCCTCTTGTTCCCCGGATTCTCCTGCATGGTCTCCAGGGCGCCAGCGAGCCGCCGCCGCCTCTGCCCCCCCTCTCCGGTGTGTTGCCCAGACCGACACCACCGCGATGAACGGCACAATTCAGACTCTTCTAATACTTGGCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019013:ENSDART00000004548:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.296
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=68.0)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=5.1)
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:
TAAAAGAGGAGGGCGACAGGG
R:
CTCCAGGGTCCAGATTCGACA
Band lengths:
357-1363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]