RnoINT0140944 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100429843-100430647:+
Coord C1 exon
chr9:100429843-100429959
Coord A exon
chr9:100429960-100430559
Coord C2 exon
chr9:100430560-100430647
Length
600 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
CTTTCTCCTTTGTGTCATAGCCT
3' ss Score
8.57
Exon sequences
Seq C1 exon
GTACCCCTGGCAGCTGTTCAGAAGACACCTGTCAGAATGGAGGCACCTGTGTCCCAGGTGCCAATGCCCACAGCTGTGACTGCAGGCCTGGGTTCAAAGGCAGACACTGTGAGCTTG
Seq A exon
GTAAGTCAGACCTGACTACTAAGCAGGTACTGGCCTCAGGGCAACTGTGATGATAGATAGCCTAGGACTTGGCCCTTGGATTTTGACCTTTCAAGATGGCTTCCCCCAAGTTGGCTTTCAACCTGTGAGGTAATAAGGCAGGGGTCCAAAAGAACTCAGGATAGTGGATGTGTGGCCTCAGAGATGAAGCGTGAACCACAGGGACAGAGGGATGCCCAAAGCACTGGTCGAAAAGCACTGTGGAACAAAGCTTAGGAAGTCAGGAACCGGGGTGGTGGTTTCATAGCAACATCTCAGGAGCCAGGCTGATGAGAGGGACAACAGATTCAGTGGGAGGACGATAAGCTCAAGAGCACATTTGGACTGAGTACCAAAAGTGCTGGAGGCTCCCAGGAAGACACGAAAGAATCCTGAGGTCACAAGGAACTTAAGGAAACCAGCCTGCAGATACTGAACACCCTGTAGCAAGTCCCAGGCCCAGAAAGTAGCTGGCACAGAGCCACAGGCTGGCACAGGTGCTTCCTGGGGGAGGGGTCTCGCTTGAGAGGTGGAAAGAACCTCCTCCTAAGAGTCAGCCTTTCTTTCTCCTTTGTGTCATAG
Seq C2 exon
CCTGTGAAAAAGTGCCCCGCCCCTGCACACGGCTGTTCTCTGAGACCAAGTCATTTCCTGTCTGGGAAGGAGATGTCTGCCACCATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=77.5)
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:
TGGCAGCTGTTCAGAAGACAC
R:
ACATGGTGGCAGACATCTCCT
Band lengths:
198-798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]