RnoINT0143824 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23760176-23760676:+
Coord C1 exon
chr12:23760176-23760250
Coord A exon
chr12:23760251-23760364
Coord C2 exon
chr12:23760365-23760676
Length
114 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
CTGGCCTGTGCGCCCCGCAGGCG
3' ss Score
9.24
Exon sequences
Seq C1 exon
CTACAGGAGTTGGTGCCCTGCCTTCCAGGGATACCATACGGTTCACCACGGCAGCCTGGGCCTCAGGGAAGAAAA
Seq A exon
GTAAGTGGACCTGCCTGGGTCCCGTGCGGGGTGGGAGCGGGTGGGATGCGGGCTGCAATAAGGAGCCCGCTGCCCCAGGGCATCCACCCTAGCACTGGCCTGTGCGCCCCGCAG
Seq C2 exon
GCGGTAGGCTGAGGCTAGTAGGCGGCCCCAGCCCTTGTCGCGGTCGCGTGGAGGTGCTGTACGCCGGAGGTTGGGGCACCGTGTGCGACGATGACTGGGACTTCGCGGACGCGCGCGTGGCCTGTCGCGAGGCGGGTTGTGGGCCTGCGCTAGGCGCCACGGGCCTTGGTCATTTTGGCTATGGCCGAGGCCCTGTGCTGCTGGACAACGTAGGCTGCACCGGTACCGAAGCCCGCCTCAGCGACTGCTTCCATCTGGGCTGGGGCCAGCACAATTGCGGCCACCACGAAGACGCTGGAGCTTTGTGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATACCATACGGTTCACCACGG
R:
CTACGTTGTCCAGCAGCACAG
Band lengths:
258-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]