DreINT0089084 @ danRer10
Intron Retention
Gene
ENSDARG00000042145 | lhx8b
Description
LIM homeobox 8b [Source:ZFIN;Acc:ZDB-GENE-081105-153]
Coordinates
chr8:17886096-17887517:-
Coord C1 exon
chr8:17887417-17887517
Coord A exon
chr8:17886192-17887416
Coord C2 exon
chr8:17886096-17886191
Length
1225 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
ATTGATTTTGTGGTCTACAGGTT
3' ss Score
7.81
Exon sequences
Seq C1 exon
GGAAATCCGTCAGTCCTGAAAAAGCATTGGCTGCTGGCTGTGAGATAAAACAAAAACCATCTAAAAGAGCACGTACCAGTTTCACTGCAGACCAGCTCCAG
Seq A exon
GTAAACAAAGCAATGCTCTCATTGTTTAATATGTCTCACACTGTGTTCTGAAATTAGAAATGAGACTTAGAAGGTTAGTTTACCTAAAAATGAAAATTATGTAATTAATTACTCACCCATCATGTCATTTCAATCCCCTGAGACATTCATCAACATCTTTAGAACATGAATTAAGATATTTTAGATGAAATCCGAGAGCTCTTTGACCCTCGATAGACAGCAATGATCCTGAAATATGACTTTGTTTTCATCTGTTTTAGATACTCTTGTTTAAAGTGACACCAGTGATCATTAAGCAAATTGCATCCATTAATGTAAACTCAACAACATTAAGCTAATTCAATTGCACCATTATTACACAGTTTGATTATAAAGAATATTTAAATCTATAAACTGTATAGATCTCTCTATGCAGGACTTTAGTTTAGGTAAAACCACACCTTTCATGGCACATTACATTAGGGATAAAGTACATCCTGGAGGTTGTTATCGCAGAATGAAGTCAGACAGGCTTATTGGGAGTCCAATACAAAGTGGAGGGCTCTTGCCTAAGACTGAAGGGCTATAATCTGTGAAAATAACCCTCCTGCATGTACTTTATCCCACTTATTACATGACTACTTGCCACAAAACATAGAAAATAGACACAAAACATTGTTCTGAGTAGTAATGGTTCATTTATTATTAAAAAATTTGATTTAAATGCGAAACTGACAGGAATGAAAACAGCAGATGGAGTACACACCAACCTGCGCATTATTCAGACACAAGAGGGCACCAAACAATTAAAAAATGCAAAGCTGACAGAAACGAAACCGGTGAATTGGAGAATAGACTAACCTACGTATGATTCATTCACATATGGTGCCCAAACAGTCAAATACCGCAACATGACAGACAAGCAGATACAAATTAATGTAGATGCAGGAATATGGATGTGAACATAGGCCTATTCATTAATATTCAAGGCGATTTGAAGTTTTCGAATGAGCCTGTATTATTCAGCAGTTGACTAGAAATAACATACTTTAGAATGTTGAGACTGACCAATCAGAATTGAGTATTCTTGACAGCAGTGTAATAAAGTAGAGTTATCACACACCCTGTATAGCTCGCAATAATAGATCCTTGTTATATTGCAGTTTGTGCATAAGGTTAGTCAAGATTTAACACTGGTTTACTTTATTGAGCTCTGCTGACACAATATTGATTTTGTGGTCTACAG
Seq C2 exon
GTTATGCAGGCTCAGTTTGTTCAGGACAATAATCCAGACGCACAGATGCTTCAGAGTCTTGCTGAACAGACTGGACTTAGTCGACGCGTCATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042145:ENSDART00000147344:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=0.123
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCGTCAGTCCTGAAAAAGCA
R:
AATGACGCGTCGACTAAGTCC
Band lengths:
190-1415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]