RnoINT0143828 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72451634-72452593:-
Coord C1 exon
chr1:72452030-72452593
Coord A exon
chr1:72451949-72452029
Coord C2 exon
chr1:72451634-72451948
Length
81 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GGGCCTCCCACCACCCCCAGGTC
3' ss Score
7.95
Exon sequences
Seq C1 exon
GGACCCCCGGCCTGGACACCATCTCAGACCCTTTCAGTTGGAGCTGGCTCCCTGGGCTGGGTAGAGATCAGGATGCCTGGCTCCCAGGAGAGCTGGCCACCAAGCCTTCTGCCAGTCTCACCTCCAGTGTGCTACAGAAAACCACAAAGGCTCCAGGGAAAGTGCCCAAGAGTACCAAGAAGTGGGTGACTAAAAATGCAAAGAGACCAACCACTCAGCCCCCTGGGATACCAATCACTAAACGCCCCAGGGTCCCAGGCACCCCAACCTCCCTAAGCCCAACCCCACGTACCTCTGAGTTACCAAAGAGACTTACTGCCGAGGCTCCTCGCAGACAGACCTCACACACCACCGAAAGGCTGACCCCTAGGGTCCCCTGGGAGTGGACCTCAGAGACCGCGGCATCACTGTCCACTCAAGGCCCCCAAGAAGTGACCTCTGAGGCCACCACCGCACAAACCCCTCAGACCTCCTTGGAGCCATTTGGTGAGAACCCAGAAGGCTCTCTAGAATCTTCCCAGGATCCAGCTGCCACCCCGACTGCTGGAGTTCCCGTGCCATCGG
Seq A exon
GTGAGTAGTAGAGAATTAAAAGGGTGGGAACAGTGAGATAGCCCTGCACCTCCTAACCTGAGGGCCTCCCACCACCCCCAG
Seq C2 exon
GTCCCTTCCGGGTTCGTCTGGCTGATGGGCCCAACAGGTGTGCTGGCCGGCTAGAGGTGTGGCATGCCGGGCTCTGGGGGACAGTCTGTGATGACAGCTGGGACCTCCGGGATGCCACAGTGGCCTGCTGGGAACTGGGTTGCGGAAAGGTCCGGCCCCGAGTAGGCAAAACCCACTATGGCCCTGGCACTGGGCCCATCTGGTTGGATGACATGGGCTGTAAGGGAAGTGAGACGTCACTGAGTGACTGCCCCTCGGGGACATGGGGGAAGCACAACTGTGACCACGAAGAAGACGTGGTGCTCACCTGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.894 A=NA C2=0.217
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCCATTTGGTGAGAACCC
R:
ATCACAGACTGTCCCCCAGAG
Band lengths:
181-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]