RnoINT0143826 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23761702-23762877:+
Coord C1 exon
chr12:23761702-23761779
Coord A exon
chr12:23761780-23762560
Coord C2 exon
chr12:23762561-23762877
Length
781 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGT
5' ss Score
8.6
3' ss Seq
GGGCCTTATCTCCAACACAGGGC
3' ss Score
5.72
Exon sequences
Seq C1 exon
GCCCAGAGGAGCTGGGACTCCAGGTCCAGCAGGATGGTTCTGAGACCACCCGAATGCCCAGTCCTCGGCCCAGAGATG
Seq A exon
GTAGGTGTCTACTGCCATTGAAAGTGAGGTTGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAGTGAGGTTGGAAATTTAGGGATAAAAACACTACAGCAATCTAGAGTTTTCTCCACTTGGGACCAAACTGAAGAGATGAGACTCCTATCTTGAAGCAGACAGTGTGAGAGAATGCACAAAGGCATGTTAGTCCATGGCTTTCACCCCAGCATTCTGGAGACTTGAGTCAGAAGAACAGTAACTTCAAGGTCAGCCTGAACCACATACATAACGACTCTACCCCAGGGAAAACACAAACAACAAATTAGCCTAAGGGAATGCAGGCATGGAGGTGGGGACAGTAAACTTTGGGGGACAGGATGAGACATGGTGTGGCTAAGGGCCTGAGGCTATCTGTTGGGGGTCTCACTGAATAGCTCTGGCTGACCATTGCTTATGAGAACAGGCTGACCTGGAACTCAGAGAGAGTCACTTGCCTCAGCCTCCCTCGTGTTGGGATCAAAGGTGTGTGTCACCTTGTCCAGCATTATTTGTGTCTGTGTACTGGTGTATATACACGACTGTATTCATACATATGTGAACACAAAACAGTATGAACAAACATGAAGGTCAGAGGACAACCCCAAGAATTTGTCTTGGTGACAAAACTGGATCCCATGAGCATATGGGCTCTTCTAACCCAGGGCCTTATCTCCAACACAG
Seq C2 exon
GGCACCTCCGTCTGGCTAGTGGAACCCACCGATGTGAAGGGCGTGTAGAACTCTTCCTGGGACAGCAGTGGGGCACTGTTTGTGATGACGCCTGGGACCTACGGGCAGCCATTGTCCTGTGCCGTCAGCTGGGATGTGGCCAGGCTCTGGCAGCCCTAGGCGAGGCCCACTTTGGCCCAGGCCGAGGCCCAATCCTCTTGGACAATGTCAAATGCCGAGGAGACGAGAGCACCTTGCTACTTTGCTCTCACATCCGCTGGGATGTCCACAACTGTGACCACAGCGAGGATGCCAGTGTCCTCTGCCAGCCATTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.019
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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTTCTGAGACCACCCGAAT
R:
CAATGGCTGGCAGAGGACAC
Band lengths:
358-1139
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]