BtaINT0141320 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030885 | SSC5D
Description
scavenger receptor cysteine rich family, 5 domains [Source:HGNC Symbol;Acc:HGNC:26641]
Coordinates
chr18:62461615-62462580:-
Coord C1 exon
chr18:62462011-62462580
Coord A exon
chr18:62461942-62462010
Coord C2 exon
chr18:62461615-62461941
Length
69 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GACCCCTCCTGATCCATGCCTCC
3' ss Score
-29.67
Exon sequences
Seq C1 exon
GAACCCCCGGCCTGGACTCCATCTCAGACCCCTTCAGTTGGAGCTGGATCCCCGGCCTGGGCAGAGACCCGGACGCCTGGCTCCCGGGGGAGCTGGCCACCAAGCCATCTGCGAGGCAGACCCCCAGCATCCCTGAGAAAACCACCAAGGCCCCAGGGAAGATGCCCAAAAGCACCAAGAAGTGGGTGACCAAGAACGCAAAGAGACCAACCACTCAGCCCCCGGCGATGCCAACCACTAAGCACTCCAGGGTCTCAGGAACCCAGAGTCCCCCTGAACTGACCTCACGGACCACCAGCACCCTGGCCACGGGGGCCTCCCGAAGACCCACCTCTGAGTTTACCACCAGGCTGACCACGCAGGCCCCCCGCAGGCTGACCTCACACACCACCGTAACTCGGACTTCTCGAGCCCCCAGGGAACGGACCTCTAAGACTGTGGCGACGCTCGCCACCCAGGGCCCCCGATTAGTGACCTCCGAGGCCACCGTGGAGCCATCCGCTGAGCTCCCAGGACAAGGTTCTCCAGAGTCATCCACGGACCCGGCCCCCTCCCCCACCGGCGCAGCAG
Seq A exon
GTGAGCAGAGGAACAGGAAGGCTGAGGCTGGCCCCTCCGGACCCCCGCTGACCCCTCCTGATCCATGCC
Seq C2 exon
TCCCACCAGCAGGCCCGTTCAGGGTTCGTCTGGCGGACGGGCCCAACCGGTGTGCCGGGCGGCTGGAGGTGTGGCACGCCGGACAATGGGGGACGGTCTGTGACGACGGCTGGGACCTGCGGGACGGCATGGTGACCTGCTGGGAGCTGGGCTGCGGGAGGGTCCGGCCTCGAGTGGGCAAAACCCACTACGGCCCCGGGACCGGGCCCATCTGGCTGGATGACGTGGGCTGCAAGGGCAGCGAATCCTCGCTGAGCGACTGCCCGGCCCGGGCGTGGGGACAGCACAACTGCGACCACGAGGAGGACGTGGGGCTCACCTGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030885:ENSBTAT00000043694:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.890 A=NA C2=0.364
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=89.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCAGGACAAGGTTCTCCA
R:
TCACAGACCGTCCCCCATTG
Band lengths:
167-236
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development