HsaINT0152592 @ hg19
Intron Retention
Gene
ENSG00000080189 | SLC35C2
Description
solute carrier family 35, member C2 [Source:HGNC Symbol;Acc:17117]
Coordinates
chr20:44985213-44986412:-
Coord C1 exon
chr20:44986262-44986412
Coord A exon
chr20:44985277-44986261
Coord C2 exon
chr20:44985213-44985276
Length
985 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GGGTGCCTGTGTCTTCACAGCTC
3' ss Score
8.96
Exon sequences
Seq C1 exon
AGCTTCCATTTCCCCCTCTTCATGACGATGCTGCACCTGGCCGTGATCTTCCTCTTCTCCGCCCTGTCCAGGGCGCTGGTTCAGTGCTCCAGCCACAGGGCCCGTGTGGTGCTGAGCTGGGCCGACTACCTCAGAAGAGTGGCTCCCACAG
Seq A exon
GTAGGTGGGGGACCTCAGTGAGGGCAGAGCAGGAAGAGGGGCTGGGGAACCATAGGATGAGAACAAGAGAGACACCCGCATGTCTGGAAGCCAAGTCCCTCCCCTCTTCCTGCACTGTTCCTCCTCTGCCCTCTTGACCTGGCCTCCCACCACCCACGCTGCTGCCTCTTGTGCACTGCGTGCCTTCCCACTGCCCCACCACACACCCACAAAACCCCCCCTGCACCTGCGGCCCCGCAGCTCCCTCTCCTGCCAGCAGACACCGAGCCTGGAGTGCAGCCCTCAGGCCTGGAGATAAGTGGTGAGCAGGCAGGGTCCCTGCCCTCGCAGGGCTGTGACACGGACATGGAGGGCACTACGGAGCCCAGGGAGGGGACCAACCCAAGGCCGGGGCCCATGGCTGGTAGAGGAAGATTTCCTAGGCCAGGTGCCAAGTAGGCAGAGCCCTGAAGGATGCGTGGGACTGGTTGGCCCTGGGAGGAGGGGCCCTCGTGGCCCGAGGGAGATTTAGTGCCAGCTGTGGGGTCTGGAAGGGAACTCAAAGTGTTTCAGGATACTGAGAACCCGGTGCTGGCCAGAGGAAGTGGGAAAAATGAGAACTGAGAGGGTGGGCAGGGGTCATGTCCTGGAGGCCGGATTCCCCGTGGAGGAGTTTGTGTTCCATCCTGAGGGAAAAGGGTTTCCAGTAAGGGATCAACCAGATCAGGTTAATACCTCCGCTCAGGGGGCTCGCCGGAGTGTTTGTGGAAACCATACCGGCCCAGCCAGTTGGAATGGGCCCCAGCCCTAATGCTAGAGCAGCCCCCGACCTTTGGGGGCCAGATATTAACCCTTTAGTTGCTGGTGGAAAAGAAGGCCCAAGGGCCCCACAGGAGGCACCGGGATGGTTCAGAAGTGGGGGACACTCAGGTGCCTCAGGGTACCAGCCCACCCCAGCAGAGTGTGGACCTCCCAAGCTGTCCTGTGGGTGCCTGTGTCTTCACAG
Seq C2 exon
CTCTGGCGACGGCGCTTGACGTGGGCTTGTCCAACTGGAGCTTCCTGTATGTCACCGTCTCGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080189-SLC35C2:NM_173073:3
Average complexity
IR-S
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(34.2=100)
A:
NA
C2:
PF0089215=EamA=FE(14.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCCATTTCCCCCTCTTCA
R:
AGCGAGACGGTGACATACAGG
Band lengths:
214-1199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)