RnoINT0143829 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72451182-72451948:-
Coord C1 exon
chr1:72451634-72451948
Coord A exon
chr1:72451350-72451633
Coord C2 exon
chr1:72451182-72451349
Length
284 bp
Sequences
Splice sites
5' ss Seq
CTGGTACCA
5' ss Score
2.73
3' ss Seq
AGCTGCCTGTCTCTCCCCAGGCT
3' ss Score
10.83
Exon sequences
Seq C1 exon
GTCCCTTCCGGGTTCGTCTGGCTGATGGGCCCAACAGGTGTGCTGGCCGGCTAGAGGTGTGGCATGCCGGGCTCTGGGGGACAGTCTGTGATGACAGCTGGGACCTCCGGGATGCCACAGTGGCCTGCTGGGAACTGGGTTGCGGAAAGGTCCGGCCCCGAGTAGGCAAAACCCACTATGGCCCTGGCACTGGGCCCATCTGGTTGGATGACATGGGCTGTAAGGGAAGTGAGACGTCACTGAGTGACTGCCCCTCGGGGACATGGGGGAAGCACAACTGTGACCACGAAGAAGACGTGGTGCTCACCTGCACTG
Seq A exon
GTACCAGGGAACAGTGAGGGAGGCCGAGGGGGTGAAGTTAGAGTGGGACAGAATGGTGTCTATGGAGCAGGCCCAGGCTGGGAAAGGGTTACCGCAGGAGACTGGCAGAGAAGAGCAGAGCAGTGGCAAGGATCGGAGGGGATGGAATTAGAGGGGACAGAATGGTGTCTAAGGAGAGGGCCAGAGGGGGTTCAGTGTGAGGACAGGAAAGGGTTACTTCAGGAAGCACAGTGGTAAGGGCCTCAGCTAGCAGGAAGAGACACAAGCTGCCTGTCTCTCCCCAG
Seq C2 exon
GCTACACAGGGGATGACGATTACCCTTCCTGGACCTGGGACCCCACTTCGGAAGAGGACCTGACCAAAAGGACCACAGTGGCCACACAGCCTGGACATACACCTTCCTGGGCTACTACCACAAACCCTGAAGTTCTCTCTCCAGCAACGCAGAGCCTTCCAGACATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.842
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGGGGACAGTCTGTGATGA
R:
TCAGGTCCTCTTCCGAAGTGG
Band lengths:
305-589
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]