RnoINT0143818 @ rn6
Intron Retention
Gene
ENSRNOG00000001435 | Ssc4d
Description
scavenger receptor cysteine rich family member with 4 domains [Source:RGD Symbol;Acc:1306970]
Coordinates
chr12:23752844-23754903:+
Coord C1 exon
chr12:23752844-23753009
Coord A exon
chr12:23753010-23754867
Coord C2 exon
chr12:23754868-23754903
Length
1858 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CCCTGTCTGGTCTGTTTCAGCGA
3' ss Score
10.72
Exon sequences
Seq C1 exon
ATGGGACCGCCTGAAAGGCCATCCCTTGGCTGGACACCCAAGGAAGCAGACATGCAAAGTGGCCCCCAGCCCGATGAATGGAGCAGTGGATGGAAGCCTGGGGATGGGGGTGCTGCCCCCTTGCCCCTCTCCCCAGCACTGTCCTTCCTTCTTCTGTTCCCACTGG
Seq A exon
GTAAGTGTCCCCAGACCTTCCCTGACACTTCTTTCTAGCTCTTGTTTCTTTCTAGCTCTTGTTTCCCACACTGTCCAACTTCGATGGGAGTCCAGGCATATTTGTAATCCCAGGACTTGGAAAGTGGAAGTAGAAGGGTCATCCTCAGCTACGTATCGGGTCCCAGGCTAGCCTGGGCTACATGAGACCCTGTCTCAAAACAACAAAAATGAGCCAGGCAGTGGTGGTGTAAGCCTTTAATCCCAGCACTCAGGAAACAGCGAGATTTCTTTGAGTTTGAGGCCAGCCTGGTTTACAGTCAGGGATACACAGAGAATCCCTGTTTCGAAACAAACAAAAAAGCCAACAATAAACAAAACCAGGATTGGCAGGATGGCTCGGCAGTAAGGGTGCTGCTTGTCACCCAGCCTGAGGACCTGAATTAGATCCCTGGAATCCATACGGTAGGAAGAAAGAGCAGCTCCTGAACATTGTCCATGGCCTCGACATGTGCCATAGGCCATGCACACGCCAACATTCATGTCCATCATTCATACACATGACACATGAATGTACACACACACATACACACACACACACACACACACATACACACACACACACACACACACACACATACACACACACACACACACACACGGTAGGAGCAGTGGGATAAAAGTTCAAGGTCATTCTCATCTACACAGTAAGTTCCAGGTTAGCCTGGGCTATGAGACTCTATCTTAAGAAATCATTAAAAAGGGACTGGAGAATACGGCTCACTGGCTAAGGCACTGGGCTGGCCCTCTTCCAGAGGACCCCAAGTCAATTCCCAGCACCCTCACAAGTGGCTCATTCGTTAATTTCAGTTCCAGGGGATCTGGTTCCCTCTTCTGGCCTCTGCCAGTACTGCATGTGGGGTACAGACCCGTGGGCAAAACACCCACACATTAAAATAAAAACACTTTAAAAACAATAGTACAAAAATGGCCAGTGAGGTAGCTAAAACCACCTATGTTCCATTAATGACAGTGATCCTTTGGCCTCCACATATAAATGCAATTTAAAAGTTTTAATTCGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAATAGAACCAAAAAAAAAAAAAAAAAAAAAAAGTTTTAATTCGGTGGCTGGAGAGATGGCTCAGTGATTAAGAGCACTGACTGCTCTTCCAGATATCCTGAGTTCAATTCCCAGCAACCACATGGTGGGATCCGATGGCCTCTTGTGGTGTGTCTGAAGACAGCTACAGTATACACACACACACACACACACACACACACACACACACACACATATATATTAAATCTTTTAAAAAATTTAATTTTTCAGTGGTGGCACATGCCTTGTAATCTCAGCACTCACTAAACTGAGGTAGGTGGAGTTCTTGAGTTTGAAACTAACCTGGTCTACAGAACAAGTTCTAGGACAGCCAGGGCTAAACAGGTAAACCCTGTCTGGAAAGAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAGAAAAAAAGAGAAGGGGAAAGAAAAGGAAAAGAAATTAATGAATTCTTAAAAAGAAAAAAGATATCAAAACTCTGCCTTGTAGAGAGAAGAGCCTCAGGGGATTTTGCTATCCAGTAAACAAATGGGTCCAGGCAGATTTGTAGAGAACCATGGAGCACTGGGATAGGGAGGTTGATGGAGCGGTCCCAGAAAAAGGAGGTGTGGGAGTTCCGGTGGTGAAACCCCTGGGGAAGGGGAAGCTTGTGAAAAGACCAGTCCTCCAGGGCTGAGCAGAGACTCACCTCCTTCCCTGTCTGGTCTGTTTCAG
Seq C2 exon
CGAGTGCCCTCCAGCCCACTCCTCTGCCCTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001435:ENSRNOT00000001953:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.661 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
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:
ATGGGACCGCCTGAAAGG
R:
CTGGAAAGGGCAGAGGAGTGG
Band lengths:
202-2060
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]