DreINT0089080 @ danRer10
Intron Retention
Gene
ENSDARG00000002330 | lhx8a
Description
LIM homeobox 8a [Source:ZFIN;Acc:ZDB-GENE-031008-2]
Coordinates
chr2:11425754-11426569:+
Coord C1 exon
chr2:11425754-11425937
Coord A exon
chr2:11425938-11426116
Coord C2 exon
chr2:11426117-11426569
Length
179 bp
Sequences
Splice sites
5' ss Seq
ACGGTACAG
5' ss Score
5.76
3' ss Seq
TTTTTTTTTTGCCTCTTCAGTCC
3' ss Score
9.47
Exon sequences
Seq C1 exon
GTTTGGTTCCAAAACTGTCGAGCTCGTCATAAGAAGCATGTCAGCCCGAACCACTCTTCAGCTGCACCAGTGTCATCACTGCAGTCGGCCCATCTCTCTCCTCCACTAATAGATGAACTTCAGTACACTGCTTTTGCCCCTGTGGACACACCAATGCTGACTGCACTACACTCCTACATGGACG
Seq A exon
GTACAGGTTTTCTTGGATTCAGCATATGCAGCTTTGATAGCATTAATTTTTCATTAGGGGTCATGCATTTTGTATAATTAGTAAAACTGATTTATTTTAATGTTTATTTTGAACTTAAACGCGTCTTAATGACTTTATGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCTCTTCAG
Seq C2 exon
TCCACTCTCCCACTTCCCTGGTGCTGCAGCCACTCCTGCCGCACTCGATGACACAGCTGCCCATCAGCCATGCCTGAGACTTCACTGCAGACCCACCGTCAGGTCAGAGGACAGCATGAGGAAATATTGACTGAGTCTTGAACAAGACCCATGCTTCTTTCTTTCATGGGCACTTACTGAAGGATTTGCAAAGATCGAAAAAAACGTTTCAGCTTAATTGTGAGAGTCTGAAGTTTTTGTTTAATATATATTATATTATCTATATAGTGATGGAATAAATGGTGTTTAATTTATTTCTTGTATGTGACTGAGCACTTTGTTTTAAAATAAATCTACCATGGATTTCTTAGTTTCTGGTTTAGTCAACACATTTTTGGTTTGTTGTGTGGTGGATCTAAAGAAAATTGGAAGCTGAAGAAAAGGCAATAAATTTAATTTTTCCACTAGTGTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002330:ENSDART00000019078:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.290 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=17.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAAGCATGTCAGCCCGAAC
R:
TGGGTCTGCAGTGAAGTCTCA
Band lengths:
249-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]