BtaINT0141330 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030885 | SSC5D
Description
scavenger receptor cysteine rich family, 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr18:62465109-62465821:-
Coord C1 exon
chr18:62465645-62465821
Coord A exon
chr18:62465427-62465644
Coord C2 exon
chr18:62465109-62465426
Length
218 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
TCTGTGTCTCCCCCCTCCAGGAT
3' ss Score
12.91
Exon sequences
Seq C1 exon
GTATGCCTCTCGGGTATGTCCCTCCCACGGCCCCCGCGGCAGGCAGCAACAGCTCAGGGCCCAGGGGGGCCCCATCCAGGTCCCCGCCCCCCACGGCGAGCCAGGCCCCGCAGATGCCCGGTGTCTCAGTTCCGCCCGCCCCCCCGACTTTCCTTCAGGAGCCTGGGCCGGATGCCG
Seq A exon
GTGAGCCCCCTGTCCTCCCCTGAACCCCAAGTGTGGGGCTGAGCATAGGTTTCCTGCCCTGCCCCTCCCACAGCCCCCTGGGCGCCCCTCCCCACTCAGAGGACAGAGGGGAGGAGAGCACAGAGCGTCTGGGCCAGCTGGGGTCTCCTCCTGGGTGAATGCACAGAGGGAAGATGGTGGAGGGCCTGCCTCAAATTCTCTGTGTCTCCCCCCTCCAG
Seq C2 exon
GATCCCCCCAGCTGCGCCTGGTGGCGGGGCCCAGCAGGTGCTCGGGCCGGCTGGAGGTGTGGCATGCAGGACGCTGGGGGACTGTGTGTGATGATGGCTGGGACCTGCGGGACACAGCCGTGGTCTGCCGGGAGCTGGGCTGCGGGGGACCGCGGCAGTCTGACCCCACTGCCGGCCGCTTTGGCTGGGGCGCCGGCCCCATCTGGCTGGACGATGTGAGGTGCACGGGGACCGAGGCTGCCCTGGCCGACTGCCTCGCCGCTCCCTGGGGGAAGCACAACTGTGCCCACAATGAGGACGTTGGAGTCACCTGCGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030885:ENSBTAT00000043694:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.883 A=NA C2=0.252
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGCCCGGTGTCTCAGTTC
R:
GTGCACCTCACATCGTCCAG
Band lengths:
292-510
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development