GgaINT0011637 @ galGal3
Intron Retention
Gene
ENSGALG00000020939 | SLC35C2
Description
NA
Coordinates
chr20:10676996-10678341:-
Coord C1 exon
chr20:10678166-10678341
Coord A exon
chr20:10677126-10678165
Coord C2 exon
chr20:10676996-10677125
Length
1040 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CATGTTTTTTCTTTCCACAGGAA
3' ss Score
12.72
Exon sequences
Seq C1 exon
GCCTGCCTTTGTCCGTATCAGAGAGGCTCTTCCACTTCCATGAAGCAGGAGTGATGTTCTGTATGGTAGGAAAGCTGTTGTTGGGTGGAATTCTTGCCTTTGGTCTAGGCTTTTCTGAGTTCCTCTTGGTTTCCAGAACATCTAGCCTCACCCTTTCTATTGCTGGTATTTTTAAG
Seq A exon
GTAAGGCATGGTTCCTGTTCTAATACTAAAGGGCAAGTACTGGGTCACCCCTAATGGGCCTAATGTGGTGGGAACTTCCTTACAGCCTCAGAAGTCGTCTGTGATTTTTATTCTCCTGACACAGGAGCTTGATGCGTTGACTTGCTGTCTCTGCAGTGAGGGCTCGTAGTCCCTGCTGCTCTGACAACAAAGGGCAGAAGCATTAAATACTGTTAAGGTCCAAAGTTTGGTGGGATCTGGGGGAAACTAGAACACGTGGGCCTCTTGAGCAATGGATGGTGTGGGAGGGAAGAGAGTTAGGAAGAACGCTTTGTTGCATCAGACCTGGATAAGGATAAACCTCTGGTTAGAGGTAACTCATTAACCTGGTTTGGCATGTTCTAAGCAAGAATCACAGAATTGCTCAGGTTGGAAAAGACCTTAAAGATTATCGAGTTCAACCACGACCTAACCAAACTACCCTACCAGCCCTCTGCTAAATCATGTCCCTGAGCACCACATCCAAACCAGGGATGGTGACTCAACCACCTCCCTGGGGAGCCTATTCCAGTGCTAAACGACCCTTTCTGTAAAGAAGTGTTTCCTGATATCCAACCTAAACTTATCCTGGCATAACTTAAGGCCATTTCCCCTCGTCCTTGCTCTCAGCAGCTCTCACTGCTGTCGCCTGTCAGCAGTAAGAAGAGACCAACCCTGCTCTGCTGTAAGCACCTTTCAGATATTAGAAGAGAGCGATAAGGTCTCCCCTCAGCCTCCTTTTCCCCGGGCTAAACAGCCCCAGTTCCTGTCCTTCCTTGACAAGTACAGTGCATGTACTTCTGAGCTGGTTGGTGACATGTGAAACTCAGCTATGTAGGAATCCTAAAACTTCCAGATTAGATGAGTGGTTCAATCAGGGGACGTAAAATCCCCGATCCCAGTTTGACAGGTTGTTCTGATTCTGCAGCCTGACATCTTGATTTAGGCTTCAGCTGCAAAATAACTTACTCACACCTCGTCAGGTCCTGTGCTGCCACTTGTCATGTTTTTTCTTTCCACAG
Seq C2 exon
GAAATCTGTGTTTTATTTCTTGCCACACACCTGCTGGGAGACCGCCTCAGTCCCTTAAACTGGCTTGGCTTTGCTGTCTGTCTGTCAGGAATCTCCCTTCATGTCATTCTCAAAGCTGTAAATTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020939:ENSGALT00000039096:9
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:
PF0315111=TPT=FE(38.4=100)
A:
NA
C2:
PF0315111=TPT=PD(23.2=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGCCTTTGTCCGTATCAG
R:
TGGAATTTACAGCTTTGAGAATGACA
Band lengths:
303-1343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]