GgaINT0011634 @ galGal3
Intron Retention
Gene
ENSGALG00000020939 | SLC35C2
Description
NA
Coordinates
chr20:10679033-10679446:-
Coord C1 exon
chr20:10679374-10679446
Coord A exon
chr20:10679202-10679373
Coord C2 exon
chr20:10679033-10679201
Length
172 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TTGTGTTTGCTCTCACCCAGAGG
3' ss Score
6.86
Exon sequences
Seq C1 exon
CTACACGATGACCAAATCCTCTGCCATTCTCTTCATCCTGTTGTTTTCATTGCTCTTCAAGCTGGAGGAAATG
Seq A exon
GTAAGGGTTCAGTGCAGTGCTTTGAGGAGGCTGAAACTCAGGCACAGGGAGGCAGGAGATACGTGCATGAGAAACATAAGTAGAGAAGGAGTGCAATTGTGTGGATGACTGGAAGAGTTAACCGTTTGGCTCTAGGAGTCCGTGTAGTGACTTTGTGTTTGCTCTCACCCAG
Seq C2 exon
AGGGTGGCATTGGTGCTGGTGGTTGTGCTCATCGCTGGGGGGCTCTTCATGTTCACCTACAAGTCCACGCAGTTCAACACACAGGGGTTCATGCTGGTGCTCTGTGCCTCTTTCCTTGGGGGTGTTCGCTGGACTCTCACACAGATACTTATGCAGAAGGCTGAACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020939:ENSGALT00000039096:6
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:
PF0089215=EamA=FE(18.5=100)
A:
NA
C2:
PF0089215=EamA=PD(14.6=33.3),PF0315111=TPT=PU(18.5=49.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACACGATGACCAAATCCTCTGC
R:
CCAGTTCAGCCTTCTGCATAAGT
Band lengths:
242-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]