GgaINT0136263 @ galGal3
Intron Retention
Gene
ENSGALG00000000365 | F1NR49_CHICK
Description
NA
Coordinates
chr22:1146438-1147245:+
Coord C1 exon
chr22:1146438-1146555
Coord A exon
chr22:1146556-1146844
Coord C2 exon
chr22:1146845-1147245
Length
289 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
CGGGCTTTTCCCTCCTGCAGGAC
3' ss Score
12.01
Exon sequences
Seq C1 exon
ATGCCCATGGATAAGACGTGGGAAAGAGGATTTGAGGTTTGGGGTGCATTGTCCTACAGCAAACCCATGTCCTCTGTGCCTCTTTGGGCTGTGGCTGCCATGGGTGCAGCACCCATGG
Seq A exon
GTAAGAAAGACAGAAGTGAGGCATTACCCAAAATTCATGCAACAGATCCCAGAAATAAAGGATTTTTCTCTTGAATTTCCACTAAACATCACAGGAAGAATTCATTTGAGTTATCCCAAGGGGCCCCATTCCCAATTTAACTCCCTCTTTGGAAACTCAGAGGCAGCAGGACTAGGTCGGGGTCTCACCGTGCTTCGGGTTTTTTGGGGCCCCTTTCCCGATTTATTTCCTCATTGGCAGCAGGACCATGCTGAGGACTCACTTGGCTTCGGGCTTTTCCCTCCTGCAG
Seq C2 exon
GACAATGTCTGCTCTCCCAGCCCTTGCAGGCAGACCAGCAGCAAACTGACCCCTGCCACCACCCCAAGCAACCGCAGCGGCGCAAACCCCGCGTTTTGTTCTCCCAAACTCAGGTGTTGGAGTTGGAGCGGCGATTCAAGCAGCAGAAATACCTCTCTGCACTGGAAAGGGAACACCTGGCCAACGTGCTCCAGCTCACCTCCACCCAGGTGAAAATCTGGTTCCAGAACCGGCGCTACAAATGCAAGAGGCAGAGGCAGGATAGATCCCTGGAGATGGCCACCTACCCACTGCCACCACGTAGAGTGGCTGTTCCGGTGCTGGTCAGAGATGGCAAGCCTTGCTTTGAGGGGTCCCAACCCCACCTGGCTCCTTATGGGATCACCGTCAGCCCCTACTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000365:ENSGALT00000040980:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.239
Domain overlap (PFAM):
C1:
NO
A:
PF0004624=Homeobox=WD(100=36.3)
C2:
PF0004624=Homeobox=WD(100=42.5)
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGGTTTGGGGTGCATTGTC
R:
ACCAGATTTTCACCTGGGTGG
Band lengths:
308-597
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]