RnoINT0143838 @ rn6
Intron Retention
Gene
ENSRNOG00000016687 | Ssc5d
Description
scavenger receptor cysteine rich family member with 5 domains [Source:RGD Symbol;Acc:1565772]
Coordinates
chr1:72455278-72457392:-
Coord C1 exon
chr1:72457228-72457392
Coord A exon
chr1:72455596-72457227
Coord C2 exon
chr1:72455278-72455595
Length
1632 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GGCTTTTTTTTTTCTTCCAGGGT
3' ss Score
10.63
Exon sequences
Seq C1 exon
GCATGCCTCTCGGTGGCGATGTGCAGCCTACAGCTCCTGCAGTGGACAGCAACAGAACAACACCCAGGCTCCAGTCTACCTCAGTGGGTCATACGCCAGGCCCAGCAGGCAGTTGGCCTCCTCCTGCTTCTCCTACTGCCCCTCCAGAGCCTGGACCTGAAGCTG
Seq A exon
GTGAGTGTTTCTCTGCTCTGGCTGTGAGACTGTCTCCATGAAACCTGCTTGCAGAAAGAAGGTAGAAAAGAGGAGCCCAAGCCCCTGCTCAGACCAGTACTTGATTTAATGGTCTGTTGATTGCGGAAAATCCAGGGTTGCTTGTACAAGAGTCCCACCTTCTGTAGCTGGCCCTGACCTGGACATGAGGATGGGCATGAGAGCTTACCATCTAACATCTGGGCTCTATGGTGGGACTGTCACAATGTCCTCTGGCTAGCCACTGACTGCTCTTCAGAGGTCCTGAGTTCAATTTCCAACAACCACATGGTGGCTCACAACCATCTGTAATGGGATCTGACAGTGTACTCTGACTTATGTATAGACACTTGTGTAAGCAGTTTTGGGGACCAAAATTAACATTACAACACTAGCAGCATTAGGTCAAACCCACTTCATTTCCCCCCTTTTGTCCAATTAACAAGGCTCTCTCTTTTCCCTCAGATATAAATTGAGCACAACCATAACAGTTATGTAAATTACAAAGTATGATGTACACGTAAGATCTAGTCCATCATATTTGTCAAAGTATTCTACCATCTATCCTAACTTAAAGAGGTTACAATTCTCTTCCTGAATTATGTTCTAATTTTAGCCTGCATTACAATCTGAAAACCACATTTTCAAATCTATGTCATCTCTCTCAGTGCTAAACAACTTGACTTTAATTATGAGACTATACCTAGTCTTCAACCCCGTCAGAAATCTGAGAATGAAATAAATATAACCTGAATATGTGGAAGCACAAAAACATAGCTTCCAAAACTTTAACAAATTGTGGAGACGTCTGACTTCCTGGACAGTTCTCTAATTTCTTATAACGTTGGAGCATTTCTCTTCAGCCTTTCGGCCCAGAACCATCTGATAGACTTGAAATGAAGCAGGAGTATAAAGGACTAGCTTACCCTGTACTGGCAGAGCTTAGCAGTTGACTACCCCACATCTGTTTGTCCTCTTTGGACAGCATTTTTGTCTGCAGATGAATAGGGCAATTCTTGCTGAGTGGTCACCGTGCCATTACTGGGTGTTTTGACGCTCAGTTGCTTCTTTGAACTGTGAGGGGGTACTCTCTGCTCCTGACATGTCTCTAGTCAAAATTTCTAATACTAATGAAATGATTAAATGTTAACAGATGCTTTCTTTCAGCTTTTAAAAATCATGTTTAGTCCTGTGTGTATATGTACACGTGTCATGATACACATAGGTCGGAGAACTCTTTCTCTGCCAGGTGGATGTCCCAGAGATCAGACCCTCAGGATTGTTAGGCTTGAGGGCAGGTGCCTTCACCCACTGAGCCATCTTGCCAGCCCCCTTTCAATATACTTTGGGTGTATCCCTAAGGGTGGAATTTCTACATCATATGGTAATTCTACATTATCTTTCTGGGGAAACACCCAGCTCTGCTTGGCTCTGTGTCCACTGCAGGCAAGACCTTGATCAGGGCCTGCTCTCTGGACTGAACGATTACAAGGAAAAGCACAGCCAAGGGAATAGATGGGCATTTAGAAAGGAAGTCATAAGGCAGGTGGATGAAGGCTCAGAGTGCTACCTGGGCTCTTTGACCCTGACTCTTGGCTTTTTTTTTTCTTCCAG
Seq C2 exon
GGTCCCCCCAGTTGCGCCTGGTGGCTGGACCCAGCAGGTGCTCTGGTCGGCTGGAGGTATGGCATGATGGACGCTGGGGGACAGTATGTGATGACAGCTGGGACATGAGAGACTCAGCTGTGGTCTGCCGGGAGCTGGGCTGTGGGGGGCCCCGACAGCCAGACCCTGCAGCAGGCCGCTTTGGCTGGGGCGCAGGCCCCATCTGGCTGGATGATGTAGGTTGTGTGGGGACGGAGGCTTCACTGTCAGAATGCCCTGCTGCTTCCTGGGGGAAACACAATTGCGCCCACAATGAGGATGTCGGGGTTACCTGCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016687:ENSRNOT00000022480:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.280
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:
TCCTCCTGCTTCTCCTACTGC
R:
CTCATTGTGGGCGCAATTGTG
Band lengths:
343-1975
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]