HsaINT0159399 @ hg38
Intron Retention
Gene
ENSG00000179954 | SSC5D
Description
scavenger receptor cysteine rich family member with 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr19:55490298-55491080:+
Coord C1 exon
chr19:55490298-55490408
Coord A exon
chr19:55490409-55490771
Coord C2 exon
chr19:55490772-55491080
Length
363 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CCTCCCTGCTCACCCCACAGAGC
3' ss Score
10.69
Exon sequences
Seq C1 exon
CCCCCCGCCCAGCTGGGAACCCCCAGAACGCCTCCCGGAAGAAGAGCCCCCGGCCCAAGCAGGCCAAGTCCACCCGGGCCCCTCTGCTGACGACAGGAGCCCCCCGCCAAG
Seq A exon
GTAAGCTCCCTGCAGGCTCCCCCGACCCCAAGGCTGGTTGCTGTGAGGCCCAGGGCCCAGAAAAACTGAGGACCTGCGGGCGCCCTCTCCTTAGCCGGGGCCCTGGAGGGATCCCAGTGTTCCCCGCGTCCCTCCCCCGGGGATTTAGACGGCCAGGCCTGGTCTCCCCTCTTCTTCCTGCCCTGTCAGGAGGCCCAGGTGTCCTGGCCCGCTCAGGTCGTGGACTCACCTCTTCACGGGCTGCCGGCGGACAGATCTCAGGCCACCGCTCCCTCAGGCCTGTTTCCCCAGGTGGAAATCGAGGAAGGGGTGTTTGAATCATTTCTCACTGGCCACACCGTCCCCTCCCTGCTCACCCCACAG
Seq C2 exon
AGCGGCTGCGCCTGGTCTCTGGCCCCCACAGGTGCGCCGGACGCCTGGAGGTCTGGCACGGCGGGCGCTGGGGCACCGTATGTGACGATGGCTGGGACCTGCGCGACGCTGCTGTAGCCTGCCGGGAACTGGGCTGTGGGGGGGCGCTGGCTGCCCCCGGCGGTGCCAGATTCGGGCCTGGTGCAGGGCCCGTGTGGATGGACGATGTGGGGTGTGGAGGAGGAGAACAGGCCCTCCGAGACTGCCCCCGAAGCCCCTGGGGCCGGAGCAACTGTGACCACAGCGAGGATGCGGGGCTGGTCTGCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179954:ENST00000389623:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.096
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=94.2)
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:
CAAGCAGGCCAAGTCCACC
R:
GCATCCTCGCTGTGGTCAC
Band lengths:
348-711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains