BtaINT0141327 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030885 | SSC5D
Description
scavenger receptor cysteine rich family, 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr18:62468397-62469149:-
Coord C1 exon
chr18:62469036-62469149
Coord A exon
chr18:62468706-62469035
Coord C2 exon
chr18:62468397-62468705
Length
330 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CCCTCCCGCCCGCCCCGCAGAGC
3' ss Score
10.87
Exon sequences
Seq C1 exon
CACCCCGCCCAGCCGGGACCCCCCAGAGTGGCTCCCGGAAGAAGAGCCCCCGGCTGCCCAAGCCGGCCAAGTCCACCAGGGCCCCAGTGCTGACTGCCGGAGCCCCCCGCCAGG
Seq A exon
GTAAGTCCGAGGCAGACCTTCCGTCTGCAACAATTCCAGAAGGGGTCAGGCCCTAGGCCCCCCAGACCAAACTGGGGACCCCAGGGTAGGGGGGCACTACGTCCCCGGGGATTCAGCCAGGCCCAGGCTCCCCGCCTGGTCAGTAGACCCGGGTGTCCACTCGCGGCAGGCCCCCAGGCTCCCTGCCCTGTCCAGACCCTGACTTTCTGCCACTGGCTGGCTGGCAGGCAGGCTGATCTCAGACCCCTGACCCCGCGGGGCCTCCGTTTTCCCAGATGGAAAACGAGTGTTAGCAGCCCCTCACAGCGCCCCCTCCCGCCCGCCCCGCAG
Seq C2 exon
AGCGGCTGCGCCTGGTCTCCGGCCCCCACGGGTGCGCCGGGCGCCTGGAGGTGTGGCATGGCGGGCGCTGGGGCACCGTGTGCGACGACGGCTGGGACCTGCGGGACGCCGCCGTGGCCTGTCGGGAGCTGGGCTGCGGGGGCGCCCTGGCCGCCCCTGGGGGGGCCCGGTTCGGCCCGGGCGCGGGGCCCGTGTGGATGGACGACGTGGGTTGCGGAGGCGGAGAGCAGGCCCTGAGAGACTGTCCCCGAAGCCCCTGGGGCCGGAGCAACTGCGACCACAGCGAGGACGCAGGACTGGTCTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030885:ENSBTAT00000043694:5
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=0.115
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=94.2)
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:
GAGTGGCTCCCGGAAGAAGAG
R:
CTTCGGGGACAGTCTCTCAGG
Band lengths:
342-672
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development