RnoINT0143837 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72457228-72458225:-
Coord C1 exon
chr1:72457908-72458225
Coord A exon
chr1:72457393-72457907
Coord C2 exon
chr1:72457228-72457392
Length
515 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
ATGTCTCTTTCCTGCCTCAGGCA
3' ss Score
8.97
Exon sequences
Seq C1 exon
GTCCTGCACCCAGGTTGCGCCTTGCTGATGGTCCCCACGGCTGTGCTGGGCGCCTGGAGGTTTGGCATGGTGGCCGCTGGGGGTCGGTATGTGACGATGCTTGGGATCTTCGTGATGCCGCTGTGGCCTGCAGGGAGCTGGGCTGTGGGGGTGCCCTGGCTGCCCCAGGGGGTGCCTTCTTTGGTGAGGGGGCTGGACCCATCATCCTGGATGACCTCAGATGTCGAGGAAACGAGACAGCCTTACGATTCTGCCCTGCGAGGCCCTGGGGTCAGCATGACTGTCACCATCGGGAGGATGCTGGGGCTGTGTGTGATG
Seq A exon
GTAAGGGCATAGGAGTGATGTGAGTGGGGAAGGCTGGAGCAGTGCATGTGTAGTCACCTGAGTGGATGGGAGAGAAGCATTGTCCAGGCTCAGCCTTCACTTCCTGTGTGATTTCCCTATCTTATATTCTTTTTTTTTTTTTTTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTGCTAGGCAAGCACTCTACCACTGAGCCAAATCCCCAACCCCCTATCTTATATTCTTATGTGAAACCTTATGCCAAGTTAACTAAGGATTGCCTAAGGGGTACTGGATATTATTTGGTATTTGATGGTCATAATGAGGGGTGAGCCCTGCTTCCTTGCTCTTAGTAGATGCCAATCTTGCCTTGCCCCCGTCTTCTTTTTCACCTCCAAACTCTACTTCCTGCTCTCTCTACCCTGTTCTTCCTACCCACTTCTTACTGCAGTTTGGGGAAGCCTTGGGCCTGTGGAGGAGGCAGCCCTGGCGGCGGTGCTAATGTCTCTTTCCTGCCTCAG
Seq C2 exon
GCATGCCTCTCGGTGGCGATGTGCAGCCTACAGCTCCTGCAGTGGACAGCAACAGAACAACACCCAGGCTCCAGTCTACCTCAGTGGGTCATACGCCAGGCCCAGCAGGCAGTTGGCCTCCTCCTGCTTCTCCTACTGCCCCTCCAGAGCCTGGACCTGAAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:7
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=1.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=91.6)
A:
NA
C2:
NO
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:
TGCTTGGGATCTTCGTGATGC
R:
GTAGGAGAAGCAGGAGGAGGC
Band lengths:
357-872
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]