HsaINT0152597 @ hg19
Intron Retention
Gene
ENSG00000080189 | SLC35C2
Description
solute carrier family 35, member C2 [Source:HGNC Symbol;Acc:17117]
Coordinates
chr20:44978177-44979529:-
Coord C1 exon
chr20:44979400-44979529
Coord A exon
chr20:44979164-44979399
Coord C2 exon
chr20:44978177-44979163
Length
236 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACC
5' ss Score
8.55
3' ss Seq
TGGTCTCTCTCTATCCCAAGGTG
3' ss Score
9.86
Exon sequences
Seq C1 exon
GAAGTCTGCACTTTGCTGTTGGCAGCTCATCTGCTGGGCGATCAGATCAGCCTCCTGAACTGGCTGGGCTTCGCCCTCTGCCTCTCGGGAATATCCCTCCACGTTGCCCTCAAAGCCCTGCATTCCAGAG
Seq A exon
GTAACCCAGAGTCCCTTCCAGAAGCCTCTGTTTTCTGTTCTTCTCCCTGTGACTCTTAGTGATTCTGATGCAGGAAGTGTGCCCGGTGGCTCTGCTGCCGTCACTCCTCTAGGAAGATGTGGGGGTCATCTCCAGAGTGGGTGGGTGGGGCCTGGGTGACTCAGCACACATGCAAATCAGAGCAAACCAAGAAAACCACGACTGGGCCTGTAACTGTGGTCTCTCTCTATCCCAAG
Seq C2 exon
GTGATGGTGGCCCCAAGGCCTTGAAGGGGCTGGGCTCCAGCCCCGACCTGGAGCTGCTGCTCCGGAGCAGCCAGCGGGAGGAAGGTGACAATGAGGAGGAGGAGTACTTTGTGGCCCAGGGGCAGCAGTGACCAGCCAGGGCAAATGGCTTAGAAGCAGGCCACTCCCCAGCCTGCTGCCAGCACTCACTGTGCTCAAGCCGCCAGGGCTCATCATGGTAGCTGGGAGCTGTGGACGGGAGTCACCAGGTGGTGGGGCCAAGCCAGGGACTCATGACTTTTGCCCCTCCCTTCAGAGCCTGGTCACACAAGGGGCGAGCACCAGGCCAGCCTGGGACTGGCCAGAGCTGGGCCCAAGCTGCGCTGGAATCGCAGCAGGAGAGGGGAGTGGGCTGGTTCTTCCCACCACTTCCCAGGCTCTGACAGCCGAGACTCATTTCCAAGGCACAGCAGCTTTCTAAAGGGACTGAGTTTGGACTGGGTTTTGGACCTCCAGGGGCTGGAGCTTCATCACCTGGGCAGTGTCTTTTCTCAGAGAGCAGGTTTCTTTATAGTTTGGAAATAAATGGTTCACGGTCCACTGGCCGCCTTGTGTTGCTGGAGACGTGGGGGCAGGGAGGGGACAGTGTGGGCCTGGCCTCTCCTTTCCTTTCCCTGCCTGGAGCCTTCTTCAAATGTCTGGTCTTAAGCCAGGCCTCCTTCATTTTCTCGCTCCTGTTAGAACACCAGTCCCCTCCCCAGTGGGGCCCCACTGCACCTGCTGGCAGGAAATAAATGAATGTTTACTGAGTACTGCATTCTGGAGACCTTACATGTTTTCACAGCCTAGTTTGAATACTGGCTTTGTCACTAGCTGTGTGACCCTAAGCAAATGACCTAACCTGTCTGTGCCGTAGTTTTTTAATCTGTGAAATGGGGATAATGTCTATCTCAGAGTCCTTTTGAAGATTGAGTCATTATTAGTAACAGATTAAATGTTATATAAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080189-SLC35C2:NM_173073:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.209
Domain overlap (PFAM):
C1:
PF0315111=TPT=PD(23.2=79.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAAGCCCTGCATTCCAGAG
R:
GGGGCAAAAGTCATGAGTCCC
Band lengths:
307-543
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)