DreINT0036769 @ danRer10
Intron Retention
Gene
ENSDARG00000035508 | barhl1a
Description
BarH-like homeobox 1a [Source:ZFIN;Acc:ZDB-GENE-050417-212]
Coordinates
chr5:29146202-29148300:-
Coord C1 exon
chr5:29148078-29148300
Coord A exon
chr5:29147174-29148077
Coord C2 exon
chr5:29146202-29147173
Length
904 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
ATGTTGTTTGTTTGAAACAGAAC
3' ss Score
7.68
Exon sequences
Seq C1 exon
TGAAAGACGAAGCTGATCGGGAAATCTCCAGCAGTAGAGACAGCCCCAACTCCCGGCTGAAGAAGCCCCGTAAAGCCCGCACCGCGTTCACGGATCACCAGCTGGCGCAGCTCGAGCGCAGCTTCGAGCGTCAGAAGTACCTGAGTGTGCAGGACAGGATGGAGCTGGCAGCATCCCTCAACCTCACTGACACACAGGTCAAAACATGGTACCAGAACCGCAG
Seq A exon
GTGAATACACACATCTTCATATGGGCTACACACAAAGAAACTAAAGTACTGAAGGAGCTGACTAGCAGTGTGCTGAACCATTTTAAAACGCGTGTTAAATAGTTAGCTTCCACACAAGCAAGAATCATTTCCAATATCAAAATTATGCAAATAAATAGCTTGAAGCAGTTTGTTTGTTGTTTCTGTTCCCGTCAAAAATTAAACCACAACGGGGAAAAAGTTACAGTAGCTACAACCTCACACTCCACGAGTCCAACACATTTAGTCATAAATAATAAATTACTGCATCGTTTATGAATAATTTAGCTTCCAAGTAGTAATTAAACAATTGCCACAATTATGAATTATTTATCCGAAAAGGCTTTTTGCTGAGTGACAATTTGACGGATGAGTGTTCAGCAGGATATTACACGGATTCATCCTCAAAACAAACTTTCCACGACGCGCCAATTTGCTCAGGGAAAAAAAAAACACTTTAAAGTCACAACGAAAATCAGCCAATGTTTTTTTTTAATTATCAATTGTAGCCAACATTTAACATCATGAGTGTTTCTTTCGGTTACTTAAGTTGATTTAAACAATCTTTTGGAGCAAAAAAAAAAAAAAAAAAAAAGAGCTTAATGTGAAAAAAAACATTGGAACATACATAAAGGGGGTCGTCTTTGTTTATTAGCGCTGTCACATGACAACAAAATGGCTTCCTGTATGTCAGTTGCGCCACACTTTGATCTGAACAAGTTTTGCAAACACTACATATTTATAACTAACAATAATTATTATTTTTATTGTTATTATAACTGCCATGAGCAGAACATTTCCCCAACGGGTTTCTGCCATTTAATAAGACTATTTAGATTTTAAAAAATGAGTAAATGAGTGACGCTATGTTGTTTGTTTGAAACAG
Seq C2 exon
AACTAAGTGGAAACGGCAGACCGCGGTGGGACTGGAGCTGCTCGCGGAAGCTGGGAATTACTCCGCTCTACAGAGAATGTTCCCTTCACCCTATTTTTATCCCCAAAGTTTGGTGTCTAACCTTGATCCGGGACCAGGCTTGTATCTCTACAGAGGGCCGTCCGCGCCTCCACCCCCTGTTCAGCGACCTCTGGTCCCCAGAATCCTCCTGCACGGGCTTCAGGGCGGCGGAGATCCAGCGTCTCTGTCCGGGGTGATCCCGCGACACCCGCCGCGATGAGCTGATCTGACCCGACCCGGCAGCCGCTCCAACCTCAGGAATCACAGGGTTGCGCTTGGACGATACCCTTGTAAAATCTAAACGCGCAATAATAGACTTTCCAAATGACTCTGACCAAAAGGCGAATGCTATAACTATTTATTAAAAATCAACGTGTGGAGGAAGTGATCAGAAAACAGTCGGATAAGGGTTCCATCACCTCATGAACCTTGTGACTTGTTTTCTGAGACGTTGCTTTTCCCTAGATTGAATGGCGTGGTTTATTTGCACAATATTATGACGCAAGCAAACCAAAATAAAACATCAACAGAAGACAATGTCAGATATGCAATAATGAAACTATTGTAGTTTTTTTTCTACCAAACGAAAAATTCATTTACTAACTAAAAGGTAAATAAATATATTAACAACAACAGGCTACAGATAATAACCATAATTGTAGCAAATGTAGGCTAATTTGTGACCAATTTATTGTGATGAAGACCGTACAGCTGAAAACCTGTTTTACGCAAATCCAGGAGTTGTCCTATAATGAAATAACACGTTGCAGCGAAAACATAATCACTGCAACCTGTTCAACGATTTAAAGCGTATTGTGGAAATATTGTGTTGTGGTTATTATGGGTTATTTACAGCCCGGTTAAACAGACGCCAAAATACTTTTCTAAATAAAGACTATCGTGACATCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035508:ENSDART00000051474:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.427 A=NA C2=0.247
Domain overlap (PFAM):
C1:
PF127672=SAGA-Tad1=FE(47.1=100),PF0004624=Homeobox=PU(89.5=68.0)
A:
NA
C2:
PF127672=SAGA-Tad1=PD(21.7=36.2),PF0004624=Homeobox=PD(8.8=5.3)
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:
TCTCCAGCAGTAGAGACAGCC
R:
AGAGATACAAGCCTGGTCCCG
Band lengths:
348-1252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]