HsaINT0152599 @ hg19
Intron Retention
Gene
ENSG00000080189 | SLC35C2
Description
solute carrier family 35, member C2 [Source:HGNC Symbol;Acc:17117]
Coordinates
chr20:44983712-44984513:-
Coord C1 exon
chr20:44984441-44984513
Coord A exon
chr20:44983881-44984440
Coord C2 exon
chr20:44983712-44983880
Length
560 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
ACTGCTCCCCATCCTACCAGCGC
3' ss Score
8.02
Exon sequences
Seq C1 exon
GTACACAATGACCAAATCCTCAGCTGTCCTCTTCATCTTGATCTTCTCTCTGATCTTCAAGCTGGAGGAGCTG
Seq A exon
GTGAGGCCCCAGCGTCTCTTGTGTCCTTCCTGCCCCCACAGATGCTAAGAATAAAGTGGGAGTCTGAGCAGTGGCTTGTCCTGCTGTGTGACAGAGGAGACAAGCCCAGTCCAGGTGGCAGTAGATCCCTTTCTGAGAAGGGACCTAGACATGGGCAATACTCAGAATATTTAGAAACCAGTGTGGCAGGGTAATGACCAAAGGTGAAAGCACTGCAGGATGAGGGTCCCAGCAGAGCTGGGTCTAGGAAGCACCCTGCTGTGGGAGGCAGTAGCCCTGTGTGTTAGGCCCAGGGAGGAGGTGGGACCACTTGGGGGCCTAGGACAGCCGTCAGTGTGGCAGAGCAAGCAGGGCTGTTGGCATACCAGCTGACCGTCAGCCCTACATGCTGACATTGGTGGGCAAGGACTGTCCAGGACCCCCTGGGATGGAGCTGAAGGGTGGAAGGATTTCTTGCCCCAGGGGCAGCCAAGATGGCTGCTGACCCCAGGCTCCAAATGTGATGAACCCTTGACCCTCAAGACCCCCGAGTTAGCTGCCACTGCTCCCCATCCTACCAG
Seq C2 exon
CGCGCGGCACTGGTCCTGGTGGTCCTCCTCATCGCCGGGGGTCTCTTCATGTTCACCTACAAGTCCACACAGTTCAACGTGGAGGGCTTCGCCTTGGTGCTGGGGGCCTCGTTCATCGGTGGCATTCGCTGGACCCTCACCCAGATGCTCCTGCAGAAGGCTGAACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080189-SLC35C2:NM_173179:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0089215=EamA=FE(16.4=100)
A:
NA
C2:
PF0089215=EamA=PD(13.0=33.3),PF0315111=TPT=PU(18.5=49.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAATGACCAAATCCTCAGCTGT
R:
CGAGTTCAGCCTTCTGCAG
Band lengths:
238-798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)