RnoINT0140947 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100435242-100437056:+
Coord C1 exon
chr9:100435242-100435323
Coord A exon
chr9:100435324-100435792
Coord C2 exon
chr9:100435793-100437056
Length
469 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAC
5' ss Score
4.29
3' ss Seq
GGTTTTCTTAATTCTTTCAGGAA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GTATAAGAAAGTCTACAAAGTTCACCAGGACGTGTGTTTTAAGGAGCGCTGCCAGAGCACAAGCCTCAAAAAGCTCAAACAG
Seq A exon
GTGCACTCTCGGGACCACGCTGTCATGCATGCACTTCTGTGGGTGGGTAGGGGTAGTACTGACAGGGTCGGTAGGCTATTTGCCCAAAAATGCAGCCCATGTGTGGCTGTACTCTGCTCAGAAACTAGTGCCCACGTGTGCATGTGTGAGGGCAGATAGGCCAGCTGTGCTTGGAGGTGGTCACTGTGGTTCTGCACAGGAATGAATGTGGTGCTGACAGGAAAACAAGGATGTGACTGACAGGCCCAAGTGTCTAAGTTGAAGTCTCCCCACAATGTCAGGTTGTTTTCTGCTCATCCCACAGCATCCTTTAGCTGGTGTGTGCACCTGGACTGAAAGGCCAGGCTTCCTGTCAGTCTGGCTGTGGGCTTTGCTGGGTTATATATGAGGAACAGATGAGGTTGGCAGAGGTAGGGTTTAATAGACACAAGATTCTTTCTCACCAAACTGGTTTTCTTAATTCTTTCAG
Seq C2 exon
GAATCAAATTAACAGTCAAACACTGAAGAAATCTTAAGGTACATTCTCCTTCATACCAAGATCTGTTGAGAACTGGAGACACCATCATACCCAGCACCTTGGACAACTGATGGTGCAAACTTAGCACTGTGCTATTACAGACCCAACCAGGAAGGTTCCAGAATTCCCTGTCTATAGCCTCCCAATAGACATAACCTGGTCTGGCCTTCCATATGAATCCACTTTCAGGTGGAAATGACTCTCTGGGGGAGGGGCAAATGCAGACCAGTTACAATGAGGCACAAGAATCACCTGGCCCCTTCAGGACAGTGGGCCTGGGTGTTAGATGGATCAAGGATGCCAAACAATCCTGGGGGTGCTAGGAAGGACCTAAGGACATACCCTCAAGCCCTATGAATAGCATTCTACTGGTGGAAAAGGGCGGGAGCCTTGTCATGTAACCTGCAGGTGATCCTAAATAGAGCCTCTCACTGGGAGAGATATCATGGATCCTGGAATTCTAAGCACTAATAACCCTGAAGTGAAAGAAACTTTGCCTGCTTGATCCAGCATGTCCCACCCCACCCTCCCCATACATAAACTGTGAGATGTCAAAGGGCATTGGAAAATTTTTTTCACAAGCCTGGGAAATACTGGGTTACACTACAGAGATCCCTGTATAGCCTGAACTCAGCCCCAACACTGACTTACTGATGGGACATCAATTGGAAACGAGAGACTGGCTGGCCAGAGACATTTCACTCCTCTCCCTTGGAGGAGCCAGAACAGTACATCTGTGCAGTGGTGGGAGAGAGGCAGATCTGGAAGCCTGCCAGGAGTGAATCACCTTTGTTCTACAGTGTAGGACGTGAAGGAGAAATGTCACCCAAAGGCCTAAGAACAAAGAAGAGCAAAGCAGTTCTGGGCGAAGGTCATCCGAAGAGAAAAGTGTCTACAGTAAAAGGCAGGGCATCAGGAGAGCGGGCTCTCAGACAGGCCTAAGCAGGGCCTGTGCATCTTGACCATTTCAGATGTGAAGACTGCAGGAAGAGCAGCTGACCAGACTCAAATCCTGTCTACTTAACAGCATCACCTTTTCACCTCAGCCCCCAAAAATGCACACAACACCCTCCAACACATGTGAGCAACTTCATTCTGGCAAAGATCAAAAATCCACAAATTATTTGGTTTTAAAATATTTACATGGCAGTAAGTCAGATGAAATATTAATGCAAAAAAAGAAATATTAATGCATCCTTTAAGAACTCACAGAAAACTCATTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTAAGGAGCGCTGCCAGAG
R:
GAAGGGGCCAGGTGATTCTTG
Band lengths:
348-817
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]