BtaINT0141321 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030885 | SSC5D
Description
scavenger receptor cysteine rich family, 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr18:62461288-62461941:-
Coord C1 exon
chr18:62461615-62461941
Coord A exon
chr18:62461456-62461614
Coord C2 exon
chr18:62461288-62461455
Length
159 bp
Sequences
Splice sites
5' ss Seq
CTGGTACAG
5' ss Score
3.91
3' ss Seq
CTCCCCCTTTTCCTCCCCAGGCT
3' ss Score
11.95
Exon sequences
Seq C1 exon
TCCCACCAGCAGGCCCGTTCAGGGTTCGTCTGGCGGACGGGCCCAACCGGTGTGCCGGGCGGCTGGAGGTGTGGCACGCCGGACAATGGGGGACGGTCTGTGACGACGGCTGGGACCTGCGGGACGGCATGGTGACCTGCTGGGAGCTGGGCTGCGGGAGGGTCCGGCCTCGAGTGGGCAAAACCCACTACGGCCCCGGGACCGGGCCCATCTGGCTGGATGACGTGGGCTGCAAGGGCAGCGAATCCTCGCTGAGCGACTGCCCGGCCCGGGCGTGGGGACAGCACAACTGCGACCACGAGGAGGACGTGGGGCTCACCTGCACTG
Seq A exon
GTACAGGGGGTGGGGCGCGGAGCGGGGGGCGGGGCACGGGGCGGAGGGGCGCGGGGCCCGGACTCGCACCTGGAGATCCTGGCAGGGGCCTCCGGAGCAGCAGCGGCAAGGACTCCTGAGACGGGTCGGGGGCTCTCCCCTCCCCCTTTTCCTCCCCAG
Seq C2 exon
GCTATGCAGACGAGGAGGACTATCCACCCTGGACCTGGGACCCCACCTCGGGGGAGGACCTGGCCAAGGGGACCACCTCTGCAGGGGTGCCCGGACACACCCTTTCCCGGGAAACCACGGGGAGCCCAGGGGCCCCCACCCCAGCAACGAGGCGCCTTCCGAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030885:ENSBTAT00000043694:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.930
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=89.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTGTGACGACGGCTGG
R:
GGATAGTCCTCCTCGTCTGCA
Band lengths:
257-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development