RnoINT0143825 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23760365-23761779:+
Coord C1 exon
chr12:23760365-23760676
Coord A exon
chr12:23760677-23761701
Coord C2 exon
chr12:23761702-23761779
Length
1025 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAG
5' ss Score
6.66
3' ss Seq
TTCTGCCCCTACTGAGCCAGGCC
3' ss Score
0.58
Exon sequences
Seq C1 exon
GCGGTAGGCTGAGGCTAGTAGGCGGCCCCAGCCCTTGTCGCGGTCGCGTGGAGGTGCTGTACGCCGGAGGTTGGGGCACCGTGTGCGACGATGACTGGGACTTCGCGGACGCGCGCGTGGCCTGTCGCGAGGCGGGTTGTGGGCCTGCGCTAGGCGCCACGGGCCTTGGTCATTTTGGCTATGGCCGAGGCCCTGTGCTGCTGGACAACGTAGGCTGCACCGGTACCGAAGCCCGCCTCAGCGACTGCTTCCATCTGGGCTGGGGCCAGCACAATTGCGGCCACCACGAAGACGCTGGAGCTTTGTGCGCAG
Seq A exon
GTGAAGCTGTGGAGTCGGATAAGGAGTGGGCGGGGCCCGACGAATAGGAAATATGGGCGGGGCACTCTGAAAGAAAAGCAGAGCAGCGCAAGCAGAGCAAGCAGGGCTGAGGGCCCATAAGAGAGGCAGTGTACATGCGCGTACCAACAATATGGGTGAGACTGAATCATGAGATGGGAGGGGGTATCCTGTGGGGGCGGAACAAGAAGTGGTTGAGCCGGGCAGTGCGTGGGCCTTCAGGGCACCATGGGCGGGGCCTCTTGCAGCAGTAAGTGGGGGTGGGCCCGAGTCTGAAAAGGCATGGGTGGGGTCGTGAGCAGGAGCTCCCTGCTGTGTGAGCGGAAGCTGGCCCAAGCCTGGGAAGAGGAAAGTGAAGCTGTGCGCAGGTTTTGTGGGCGGGATGGTCTGAGGTTTTTTTGTGGGTGGAGCCTCTTAGCGGGCGCTGCGGTAAGGGCTAGACAGGGTCTGATCTGGAATAGAGGAATAGGCGTGGCACTCTCTGCTGCACTGCAGCGGAAGTATTGCGCATAGCGGGGGTAGCCGGATGCTGGGGCACTCTCAGCGGCTGAGCCGTAGGGGCGTAACCGGAAGGGCGAGTTCTCTGCAGGGTGAGAATAGGGCGCGGCCAAGGGAGGACTCGAGCGGTGCTTTCTAGTTTATAACGGCTGTGTCGTTTATTCTCTCCCTGCTGAGTCAAGGTTCCTACTAACTACTAGTGATTGGTAGGAAGCAGGAGGGGCGGACTGTTCTCCCAGAGCTAGCCTTTTCAGAGATAGCAATGAAAAGAGGCATTTACAGAGTCTGGCAGGACATTGTCAATCCCTTCTGTTCTCGCTTGCTGTAGAAGGTGGAATCTCCACCTTTACTTGATGCCCAGGTGGCCCTTCAGTCTCTTACCTTAGGGGACAGTTCTTTGAGGTTCTTTTCTTTCTGTAAAACCTGGGAAAGTTAGGAGAGATGATCTGGCTCTAGATAGCATGTTCCCCACCGTGACAGCCATCTTTTTTCTGCCCCTACTGAGCCAG
Seq C2 exon
GCCCAGAGGAGCTGGGACTCCAGGTCCAGCAGGATGGTTCTGAGACCACCCGAATGCCCAGTCCTCGGCCCAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:8
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=0.667
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=93.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTAGGCTGAGGCTAGTAGGC
R:
TGGTCTCAGAACCATCCTGCT
Band lengths:
358-1383
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]