HsaINT0159393 @ hg38
Intron Retention
Gene
ENSG00000179954 | SSC5D
Description
scavenger receptor cysteine rich family member with 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr19:55500490-55501201:+
Coord C1 exon
chr19:55500490-55500804
Coord A exon
chr19:55500805-55501033
Coord C2 exon
chr19:55501034-55501201
Length
229 bp
Sequences
Splice sites
5' ss Seq
CTGGTACCA
5' ss Score
2.73
3' ss Seq
TTACCCCAATTTCTCCAAAGGCT
3' ss Score
7.7
Exon sequences
Seq C1 exon
GCCTGTTCCGGGTTCGTCTGGCCGATGGGCCCAACCGCTGTGCTGGCCGGCTGGAAGTGTGGCATGCCGGACGCTGGGGAACAGTGTGTGATGACAACTGGGACCTGCGGGACGCCACTGTGGCCTGCTGGGAACTGGGCTGTGGAAAGGTCCGGCCTCGAGTAGGCAAAACCCATTACGGCCCTGGGACTGGGCCCATCTGGCTGGATGACATGGGCTGTAAGGGAAGCGAGGCCTCACTGAGCGACTGCCCCTCGGGGGCTTGGGGGAAGCACAACTGTGACCACGAGGAAGACGTGGGGCTCACCTGCACTG
Seq A exon
GTACCAGGGCATGGCGGCGGTGGTGGGGTTGTCGGGGGTGGCCAGGAGAATGGAGTCAGGGTGGGGCCAGGTGACGGCACCATGGTCGACTCTAAAGAACTGGGTATGAGGGGTCGGGGTGGGGAGATCCCAGAGTTGCTCCAGAAGATTCCAAAAGGGGAGGGAAGAGCAGCAGCAAGGACCTCTGAGAAAGAGGATGGGGTCAACCATTACCCCAATTTCTCCAAAG
Seq C2 exon
GCTACACAGACTATGACGATTATCCCCCCTGGACCTGGGACCCCACCTCAAGAGAGGACCTGGCCAAGGGGACTACCACAGCGGGGGTACCTGGACACACTCTCCCCTGGAGGACCACCCGGCGCCCGGGTAGCTCCTCCCCAGCAATAAGGCGCCTGCCGGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179954:ENST00000389623:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.165 A=NA C2=0.807
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGGCAAAACCCATTACGGCC
R:
TATTGCTGGGGAGGAGCTACC
Band lengths:
302-531
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains