HsaINT0159397 @ hg38
Intron Retention
Gene
ENSG00000179954 | SSC5D
Description
scavenger receptor cysteine rich family member with 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr19:55489354-55489995:+
Coord C1 exon
chr19:55489354-55489662
Coord A exon
chr19:55489663-55489881
Coord C2 exon
chr19:55489882-55489995
Length
219 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TCCCTGCCCCCCCGCCGCAGGTC
3' ss Score
10.53
Exon sequences
Seq C1 exon
AGCGCCTGCGCCTGGCCGATGGCCCCCATGGGTGCGCTGGCCGCCTGGAGGTCTGGCATGGCGGGCGCTGGGGCACCGTGTGTGATGACGGCTGGGACCTGCGCGATGCCGCCGTGGCCTGCCGGCAGCTGGGCTGCGGAGGGGCACTGGCCGCCCCGGGAGGCGCCTTCTTCGGGGAGGGGGCAGGGCCTGTGTGGCTCAGCGAGCTGGCTTGCCGGGGCAACGAGGGGCAGCTGGGCCTCTGCCACCACCGGGGCTGGAAGGCCCACATCTGCTCCCACGAGGAGGACGCGGGCGTCGTCTGCGCAG
Seq A exon
GTGAGGACACCCTGGCTGCTCCTTCAGGGGGAGCTCCTTTGGAGATGACCCAGGAACCCCAAGTCCTTAGCCCCAGCAAGTCTGAGTGTTCAGCAGTTCAGAGACACCCAACCTCCCATCCCCTCCAAAGCCAGGTGGCTAACTCCCTCTTCCAGGGACCCAAATGGCCTGGATTCCCCTCCTCTCCTCATAGCTTCTGTCCCTGCCCCCCCGCCGCAG
Seq C2 exon
GTCAGCGTGTGGCTAACTCCAGGGACGACTCAACATCTCCCCTGGATGGGGCTCCCTGGCCAGGGCTGTTGCTGGAGCTGAGCCCCAGCACGGAGGAGCCCCTGGTGACACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179954:ENST00000389623:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.718
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=94.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGAGGTCTGGCATGGC
R:
TGTTGAGTCGTCCCTGGAGTT
Band lengths:
301-520
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains