BtaINT0141329 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030885 | SSC5D
Description
scavenger receptor cysteine rich family, 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr18:62465645-62466387:-
Coord C1 exon
chr18:62466070-62466387
Coord A exon
chr18:62465822-62466069
Coord C2 exon
chr18:62465645-62465821
Length
248 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
TCTCCCCTCCCATTTCCCAGGTA
3' ss Score
10.68
Exon sequences
Seq C1 exon
GCCCGGCCCCCCGGCTGCGTCTGGCCGATGGCCCCCACGGGTGTGCTGGCCGCCTGGAGGTGTGGCACGGCGGGCGCTGGGGCACCGTGTGCGATGATGGCTGGGACCTGCGGGACGCCGCCGTGGCCTGCCGGGAGCTGGGCTGCGGGGGCGCGCTGGCCGCCCCCGGGGGCGCCTTCTTCGGGGAGGGCGCGGGGCCCATCCTTCTGGACGACCTCCGCTGTCGGGGGAACGAGACGGCCTTGCGGTTCTGTCCGGCGCGGCCCTGGGGCCAGCACGACTGCCACCACCGGGAGGACGCCGGGGCCGTGTGTGATG
Seq A exon
GTGAGGGTGGCCCTGGGGAGAGGCCAGGGAGGGAGGCCTGGGGGGCTTCGCCCGGAGGGGTGAGAGCTGGGGTGCTGTGTGTTTTCCGAAGGTTACCCCCGGTGTCCCCACTCCTTCCATCTAGGTGGCCCGCCACCCCATTCATGCTCACCTGTGAATCCCCACCATAGTGGTCCTGGGCTGGTGGTCGGGGAGCCGCCCGCCACACAGCAGGGGCTGGTGGTCACCTCTCCCCTCCCATTTCCCAG
Seq C2 exon
GTATGCCTCTCGGGTATGTCCCTCCCACGGCCCCCGCGGCAGGCAGCAACAGCTCAGGGCCCAGGGGGGCCCCATCCAGGTCCCCGCCCCCCACGGCGAGCCAGGCCCCGCAGATGCCCGGTGTCTCAGTTCCGCCCGCCCCCCCGACTTTCCTTCAGGAGCCTGGGCCGGATGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030885:ENSBTAT00000043694:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.883
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=91.6)
A:
NA
C2:
NO
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:
GGGGCCCATCCTTCTGGAC
R:
CCCAGGCTCCTGAAGGAAAGT
Band lengths:
292-540
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development