GgaINT0011637 @ galGal4
Intron Retention
Gene
ENSGALG00000020939 | SLC35C2
Description
solute carrier family 35 member C2 [Source:RefSeq peptide;Acc:NP_001026036]
Coordinates
chr20:11072400-11073745:-
Coord C1 exon
chr20:11073570-11073745
Coord A exon
chr20:11072530-11073569
Coord C2 exon
chr20:11072400-11072529
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:ENSGALT00000039096:11
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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]