RnoINT0143819 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23754868-23755363:+
Coord C1 exon
chr12:23754868-23754903
Coord A exon
chr12:23754904-23755057
Coord C2 exon
chr12:23755058-23755363
Length
154 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TTTGTCTCCGTTTTTTACAGAGC
3' ss Score
10.49
Exon sequences
Seq C1 exon
CGAGTGCCCTCCAGCCCACTCCTCTGCCCTTTCCAG
Seq A exon
GTAGGTTCTGCCACTTCCCCCTCATCTGTTCATAGATATTCCCAAGCTGGCATAGTCCAGCCATACCAGTTTGGGAGAAGGCTCCCGTGGCATCCTTTGGCATCCCGTGGGTTCCCGATTCCTCACTGCACCCGTTTGTCTCCGTTTTTTACAG
Seq C2 exon
AGCTGAGGCTGGTAGGGGGTCCAAGCCGCTGCCGAGGGCGCCTGGAGGTCATGCACAGCGGTTCCTGGGGCAGCGTTTGCGACGATGACTGGGACGTTGTGGATGCCAACGTGGTGTGTCGTCAGCTGGGCTGTGGCCTGGCATTGCCGGTGCCGCGGCCCCTCACCTTTGGCCAGGGCAGAGGGCCCATTTTCCTGGATAATGTGGAATGCCGCGGGCAGGAAGCGTCTCTGAGCGAGTGTGGCAGCAGGGGCTGGGGTGTCCACAACTGCTTTCACTATGAAGATGTGGCGGTCCTGTGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:2
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=95.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCAGCCCACTCCTCTG
R:
CGCGGCATTCCACATTATCCA
Band lengths:
245-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]