RnoINT0143833 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72459722-72460403:-
Coord C1 exon
chr1:72460095-72460403
Coord A exon
chr1:72459836-72460094
Coord C2 exon
chr1:72459722-72459835
Length
259 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAA
5' ss Score
6.02
3' ss Seq
ACTTTGCTTCTCTCCCATAGGTC
3' ss Score
12.57
Exon sequences
Seq C1 exon
AGCGACTCCGCCTGGCTGATGGCCCTCATGGCTGTGCAGGACGCCTGGAGGTCTGGTACAGCGGGCGCTGGGGCACCGTGTGTGATGACGGATGGGACCTTCGGGATGCTGCAGTGGCCTGCCGTGTGTTGGGCTGCGGAGGGGCGCTAGCCGCCCCCGGGGGTGCCTTCTTTGGGGAGGGCACTGGGCCCGTGTGGCTCAGTGAGCTGGCCTGTCGGGGCAGTGAGGGACAGCTGGGTATCTGTCCCCACCGGGGCTGGAAGGCTCATATCTGCTCTCACGAGGAGGACGCGGGCGTCGTCTGTGTAG
Seq A exon
GTAAAAAGATTCAAACTCCTCTTATGGTTCTGGCCCCAGGAACCCCCAAGCCCTTAGTTCCCACAGATCTGAGCTGTCTGGAAGCTGAGAGATAACCAATTCCAGATCTCATAAGGCCAGGTGCCCACCCCCAAAGACTGCCAGCTTATTTCTGAGCCCCAGGGAATTCAGGCATCCAAGGTCCTTCTGCCCCAGGGGTCAAATGGCCCTTCTACTCCTCCCCCATCACTGTCCTCATAACTTTGCTTCTCTCCCATAG
Seq C2 exon
GTCAGCGTGCAGCTAACTCTAGAGAAGACTCAGTGTCCCTGCTGGATGGGGACCCATGGCTGGCACTGTCTGGGGAGCTGAGCCCCAGCTCAGAGGAGCCCCCTATAACTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.487
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=94.2)
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:
GTGTGTGATGACGGATGGGAC
R:
CCAGACAGTGCCAGCCATG
Band lengths:
305-564
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]