RnoINT0143835 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72458715-72459494:-
Coord C1 exon
chr1:72459381-72459494
Coord A exon
chr1:72459024-72459380
Coord C2 exon
chr1:72458715-72459023
Length
357 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TCCCTGTCTGCACCCCCCAGAGC
3' ss Score
7.91
Exon sequences
Seq C1 exon
CTCCCCAGCCGGCAGCAAGCTCCCAGAATGGCCCCCGAAAGAAGAACCCCCGGCCACCCAAGCAGGTCAAGTCCACCCGAGCCCCTGTACTGACAAATGGAGCTCCCCGCCAAG
Seq A exon
GTAAGTCTCTAAATCTCCCTTAGACAAGGTCCTGATCTGGGTGCTATGAGACCCTAGACCCGGCCAAACTGAGGATCCCAGACCTCCATTCAGCCAATGACTCTCCAAGGAGACCAACATTCATTGTTTCCTCCCTTCAGATCCAGTCAGGGCTGGCCACCCCCTCTTCTTGATCCTTCCTCTATGAGAACCAGAGGGATAGCAGTTTTCTTTTCTAAATTAGCCAATCGGCAGGCAAACCTCAGTCCTCTGCTATTTCTGGGCCTTAGCTTCCCCAGGTGAACAAACAAGAAGCTGCCCCTCCAAGCTGACATTAGCCTCATACGGTCTCCTGTCTTCCCTGTCTGCACCCCCCAG
Seq C2 exon
AGCGGCTGCGTCTGGTCTCAGGTCCCCATGGATGTGCCGGCCGCCTGGAAGTCTGGCACGGTGGACGTTGGGGTACTGTCTGCGATGATGGATGGGACCTCCGAGACGCAGCAGTGGCCTGTAGGGAGCTAGGATGTGGGGGAGCGCTGGCCGCCCCTGGAGGTGCCAGATTCGGACCTGGTGAGGGACCCGTGTGGATGGACGATGTCGGGTGTGGAGGAGGAGAGGAGGCCCTCCGGGACTGTCCCCGAAGCCCCTGGGGCCGGAGCAACTGTGACCACACAGAGGATGCAGGGCTGGTCTGTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:5
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=0.139
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:
CAAGCAGGTCAAGTCCACCC
R:
CTGCATCCTCTGTGTGGTCAC
Band lengths:
350-707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]