GgaINT0050662 @ galGal3
Intron Retention
Gene
ENSGALG00000018439 | E1C1N2_CHICK
Description
NA
Coordinates
chr7:19244061-19245023:-
Coord C1 exon
chr7:19244611-19245023
Coord A exon
chr7:19244198-19244610
Coord C2 exon
chr7:19244061-19244197
Length
413 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TGCACCGTTTGTGGTTGTAGGGG
3' ss Score
6.74
Exon sequences
Seq C1 exon
TGTTCCGCTTAAATTGGGTTCTTTCCCGTCCTGAGAAACACAACAGACCCCCAAAAGGCACGCTGAAGAGAGAGCACACACACAGACCCAGCGGCGAGAAATGACCATGACCACCATGCCTGAGAGTCTAAACAGCCCCGTCTCGGGGAAGGCCGTCTTTATGGAGTTCGGGCCGCCCGGCCAGCAAATGTCTCCTTCTCCCATGTCCCACGGACACTATTCCATGCACTGTTTACACTCGGCGGGCCACTCGCAGCCCGACAGCGCGTACAGCACAGCTTCGTCCTTCTCCCGACCGCTGGGCTACCCCTATGTGAACTCGGTGAGCAGCCACTCCGGCAACCCCTACATCAGTTCAGTGCAGCCCTACCCCAACAGCTCCGGCCTGGCCCAGCCCCGGCTGGAGGAGACAG
Seq A exon
GTAGGTGCCGGGGGCGGGGGGCGCGGAGCGAAGCAGATCCGCCGGGGGGGGAGCGAGGCGGCAGCGCGGAGCCGTGTGTGAGCCGGGCGGGGCCGCGGCCGCGGGGAGCGGGCGCCGAGCGGAGCGGACCCAGCCCAGCTGCGCGCGGAGCGGTCCCCGTCATTATTTATTGCGTAGCGCTATAAACAATGTACGCAATTAAGGGTAATTAAACCTCGACTGCAGCCGGTAAAAATAGCAAACTTTGCTGGGATGGAGCCGGGGCTGCCACCGCCGCGCGGAGCCTTTGTTGGCGCTGCGGCGCTCCGCCGCCCCGTCGCCGTGAGCGCTGCGCTGTCGCCGTCGCCGTCGCCGTTACTGCTGTTCTCTCGCTGCTATCACTGTTATTTACTGTGCACCGTTTGTGGTTGTAG
Seq C2 exon
GGGCCGAATCGGAGAAAAGCACTGTGGTAGAAGGAGGGGAAGTTCGCTTTAATGGGAAAGGGAAAAAAATCCGCAAACCCAGGACTATTTATTCCAGTTTGCAGCTGCAGGCTCTGAACAGGAGGTTCCAGCAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000018439:ENSGALT00000006647:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.781 A=NA C2=0.572
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(35.6=45.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGAGTCTAAACAGCCCCGT
R:
AAGCGAACTTCCCCTCCTTCT
Band lengths:
342-755
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]