DreINT0036773 @ danRer10
Intron Retention
Gene
ENSDARG00000104361 | barhl2
Description
BarH-like homeobox 2 [Source:ZFIN;Acc:ZDB-GENE-050913-153]
Coordinates
chr6:24720280-24721872:+
Coord C1 exon
chr6:24720280-24720505
Coord A exon
chr6:24720506-24721339
Coord C2 exon
chr6:24721340-24721872
Length
834 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
GTATTTTGATCTCATTACAGGAC
3' ss Score
8.04
Exon sequences
Seq C1 exon
GAACAAAAGAAGAGGGCGATCGGGAAATTTCTAGTTCCAGAGACAGTCCACCAGTCCGTTCTAAAAAACCTCGCAAAGCGCGGACGGCCTTCTCCGACCATCAACTTAACCAGCTGGAGCGCAGTTTTGAGAGACAGAAATACCTCAGTGTACAGGACCGAATGGACCTGGCAGCAGCCCTAAACCTCACAGACACACAAGTAAAGACTTGGTATCAAAACCGACG
Seq A exon
GTAAGTGTCATATTAATATTTATGAATATTATTTTTGTTATGGCTCACATAATAATAATAATACTAATAATAACAATAGTAAAATTGCATTTTTTATTTTATTGTTTTGTATCTGCATTTAAATCTGTTTTACAGTTGCCAAAAGTTGAGATTTAAATTTTCGGATTTTATTTAGGCTATTTATCAAAATGTATTATTATGTTATTACTGGTATATATATATTATATTGGTTACGCATTAATTTTATTAAACAGCATTTTTTTAAATAAACGATGCAACCTAATATGAATCAAATAGCTTTCACAGGCTGTCGGAATTTATATTTTATATATATTCACATTAAAGGATTAAAATTTAAATTGTTTAAATTATCATGATCAGTAATAGGCTCAAAATTATCTTCCTTTCCTTCCCAAATGCTTTTTCTTTTTTAGTATTGATTAGATTTTTAAGTTATTACATTTATATAAGTAGCATTATATTCATTATTACATTTATTATTACATGTATTATTCTCTCAGCTATTTAGTAAATTTATCGTATGGTAACTGTACTAGAAATCATACCTTGGTTAAATATAAAAGCAGGTTATATCAACGTGAATAAATAAAATAAATACAAACTAAAATAATAATTTGTGACCAAAAAACTAGTAGCATGTTTCTCGTTTTCTTTTCTTTTCATTTTACCTTTCAAGCTATTTAGGCCCGTTGCTTAAAATTAAGCTTACCCAATTAGGTTTGTGCCAGAATCAAACATATTGAAAAATCTGGCCCATAAGGTGCCATGTGGATAGTTTAATAATTGATTTCGTGTATTTTGATCTCATTACAG
Seq C2 exon
GACGAAATGGAAGAGGCAGACGGCTGTCGGATTAGAACTGCTGGCTGAAGCTGGAAATTATTCGGCCTTACAGAGAATGTTTCCTTCCCCGTATTTCTATCATCCGAGTTTATTAGGAACCGTGGACAGCACGACAGCGGCCGCAGCCGCCGCTGCCATGTACAGCAGCATGTACCGGACTCCGTCCACACCGCATCCGTCTCTCCAGAGACCGCTCGTCCCCAGAGTGCTTATTCACGGCCTGGGGCCCGGGGGACAACCGGCACTAAACCCCATACCAAACCCAATTCCGGGCACACCGCATGCTCGGTAAAACAAGAAGACACTGAGAGACAAATGTATCACAAGTGATGTGACAGACTGAACTTTCACAGAAGCTTTTTTTCCTAAAAAAAAAAAAAACAAAACACCGAGAGACGATTTTTATCGAAGACAAAGATGTATTATTTAATATGGACCATTTCTGACTTATAGGCCAAACTGAACCAGTCGAGCCTGTGACCGTGACAGTAAAAGGACTGTTCATTGTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104361:ENSDART00000165609:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.592 A=NA C2=0.298
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=67.1)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=4.8)
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:
GGAGCGCAGTTTTGAGAGACA
R:
CCGTGAATAAGCACTCTGGGG
Band lengths:
351-1185
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]