GgaINT0144019 @ galGal3
Intron Retention
Gene
ENSGALG00000002996 | HXB5_CHICK
Description
NA
Coordinates
chr27:3586249-3586620:+
Coord C1 exon
chr27:3586249-3586284
Coord A exon
chr27:3586285-3586372
Coord C2 exon
chr27:3586373-3586620
Length
88 bp
Sequences
Splice sites
5' ss Seq
GGTGTATAT
5' ss Score
-4.8
3' ss Seq
TTGTTGTCCGTGTTATTCAGACA
3' ss Score
6.42
Exon sequences
Seq C1 exon
GTGAATCTTTTACCTCGGTGTTAAATATACGTAGGT
Seq A exon
GTATATATATATAGCCGTAATGATAAAAAACCCTGGCAGAAAGAGTTGAAGAGAAATTCAAAATCCCGTTGTTGTCCGTGTTATTCAG
Seq C2 exon
ACATGACTGGACCAGACGGGAAGAGGGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGGAGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAATGGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002996:ENSGALT00000021590:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.134
Domain overlap (PFAM):
C1:
NO
A:
PF0004624=Homeobox=WD(100=68.7),PF099744=DUF2209=WD(100=55.4)
C2:
PF0004624=Homeobox=WD(100=68.7)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCGGTGTTAAATATACGTAGGT
R:
TTTTGATCTGCCTCTCGGAGA
Band lengths:
181-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]