GgaINT0144541 @ galGal3
Intron Retention
Gene
ENSGALG00000001978 | MED16
Description
NA
Coordinates
chr28:2325325-2326140:-
Coord C1 exon
chr28:2325934-2326140
Coord A exon
chr28:2325536-2325933
Coord C2 exon
chr28:2325325-2325535
Length
398 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
CTGCTGCCTCTGTCCCTCAGGTC
3' ss Score
11.14
Exon sequences
Seq C1 exon
CTGAGCATGCTTCGTATCTCCCCCTCCATGGGCCATGTGCTGGACATGAACACCTCCCTCCGCCACTTGCTGTTCCTGTTGGAGTACTGCATGGTGACTGGCTACGACTGGTGGGACATCCTGCTCCACGTCCAGCCCAACATGGTCCAAAACCTGGTGGAGAAGCTGCATGAAGAGTACACACGGCAGAGCGCAGCCCTGCAGCAG
Seq A exon
GTCAGCAAGAGTGGAATCTCCCTGGTGTACAGCAGAGGGAGTGGGCACAGGGAGAGGTCTCAGCCACAGGGAGAGGGCTGTAACAGTGTGGCTGTGCTGTCTTGGAATGCTCTACACTGAGCAGTGCTTGAGGTGTGAAGAGCTGCTTTTGACACAGTGTTTGTTGTCACCAATCTCTCCCTGTTGGGAAGTTCTGGTGAGATGTTAGAGACTATTTTTGACGGAGGTCACGTCAGCATACTGGGAACAATAGAGGACTGTTTGTACATGCATGAAACAGCACTCACTATCCCAGTTGCTCACACAGCAGAGGTGCAGAACAGAGAATAGAGCAGTTTATGAGCTGATCCTCGTTCTGCCTTCCATCCTGAATGTTTTCTGCTGCCTCTGTCCCTCAG
Seq C2 exon
GTCCTGGCCACACGCATTGTTGCCATGAAGGCATCTCTTTGCAAGCTCTCCTCCAGCACGATAGCCCGTGTTTGTGACTACCATGCCAAGCTGTTCCTCATTGCCATCAGCTGCACCCTGAAGTCACTGCTGCGCCCTCACTTCCTCAACACCCCGGATAAGAGTCCTGGGGATCGACTCACAGAGGTCTGCTCCAAGATCACAGATATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001978:ENSGALT00000003081:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF116353=Med16=FE(9.5=100)
A:
NA
C2:
PF116353=Med16=FE(9.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACTTGCTGTTCCTGTTGGA
R:
TTGGAGCAGACCTCTGTGAGT
Band lengths:
342-740
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]