RnoINT0140943 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100426766-100429959:+
Coord C1 exon
chr9:100426766-100426861
Coord A exon
chr9:100426862-100429842
Coord C2 exon
chr9:100429843-100429959
Length
2981 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ACAGTCTTTCCTGTTTCCAGGTA
3' ss Score
10.26
Exon sequences
Seq C1 exon
AACCCACTACTCCGGTGCCGCTCAAGAACACAGAGGCCCCTGAGCAGGCCCGTCTGGCCCTTCAGCTACCCAAGAACAACAGCAAGGACACAGAAA
Seq A exon
GTAAGTCATGTGTGTGGAAGGGAAGGGGGCTGGTTGTTCTCCATAGCTACTATGGTGAGAGGCACCACAGTGGAAAGCTGCGAAGTATCAGGTCTGCCCAAGGGAGTTGGCACTGCAGCTGAGACAATCTCCCACTTCATGAGAGGCCAGAGAGCAGGACACACACAGGATCTGTCTTAGAAAGGCTGGGCCACTCTCCTTATTTCCAGTGACCCCCCACCTTGCCCCTCCTCACCCACTTTGGGGATCCACTTCAGGCCACCCAGCTCACTTCCTAGAGGAGGTGGACATCAGTGAAGAGTGGCCATTGAGCAAACCCTGGCTTGAGGAATGCTACCCCAAGCTTGGCAAAATGTAGGGCTACTTGTAGCCTAGACTGTTCTGTCCCCACGTAGCACCAGATGATTCCAGGACCTCTGGGCAAGCAGCCAGCAGCGCAAACAGATGCCTCTTCAACTGTCAGGCTCTTGCTCTGTCCTTCGCCCTCTAAGCCCTCTAGGGATTATGGATTAGATTCCAAGGTCCTCCTTCCTCCTCCTGAGTCAGACACTTAAGACTCTGTTCACCTAGCCCCACAAAGACCAGAGTACTTGGTGGAGGTGTAAGCCCCACAGTAACCTCACCTGAGAAACTGCCCTGGAAGGACAGCTGTTCATATTAAGGATGTTACAGTGCCAGAGGTACAAACAGAGGGCCCACTGATCCTGAATTAAGTATTCTCCCCACCCTGGGACACCCGTACCAGCTCTTGACCCTGTGCACCCTGGGAGGGTGGCTGTGCATGCTGTGGCATGGAAACACTCCTGACCAGTTTGTCCTGCTTTCTGAGAAGATAAGGCAGGCTCACTGGACAGTTACCTTGGCCCTGTGAGTACCAGTTGTTCCCTTTCATAAAGCCCAAAACAGTCTGTTTTCCCTATGGGTTCAGTCTCCTGGGCTCCATCTCAAAAAGAAATCCAAGTGGCCCCAAGGCCATTGTCACCCTGCAGTGGGGTACATTTCAGTGACATTACAAGAAAGAGAACCCCTTAAGGCCTCAGACACAAAACTACTCATGACCTTCGGTTCCTGTCACACCCATGCTGTCTGTCCATCTGTCTGTCATTAGGTTGCCTTTGATAATGATGGGTCCTGGCCCATGCTAGAATCTGGTAGGAAGTTAGTCTTGTGGTTTTTCTCCTGGGCCCTGCATGCAGCCCACTCTGTCCTGCACTCTGAGTCCTTAGTCTTAGAGAGGCTGGATGGTAGGGGTGGGAGGGGTGTGTCACACATGACAACAGAGAGTCCTCTGTAAGAAACACACTCTAACCCAGCTCTTGGTCACCTGAATCAAGTGTCCCCACATGCGTGGGTCTATTCTGGGCTGTCTCCTTTGTTTCAGCATTTCCCTTCTGTGAGCCAATTCATCTAACTTAATGTCGCTGGCCTTCGGTGTGAACCTACTACATACTGAGGACCTCGAAGGGTCTCAACCTTCCTTTCAGTTGTCCTTCCTTCTCTGTATGCTGGCCTTTGTCTAGTACACAAGGAAACAAGCTCTGAAGGCCGTGTGTGCCCACACACATTTCTCAGCCCTCACTCAGTATGCCAGGTTCAGATTCCTCTCTCCACTGTCATCTGGTGTCAGTCTTGTTCTCGTTTCCTTGTAGGTCATCTGACCCTTTTCTCTGCAAGAGTTGGACTTTTCTTCCCTGAGTAAAAGAGTATCCCCCAAAAAGCCCTCAGGAGTCCCTAAAGCACATTAATGCCCCCAAAGGGTGTTTCCTCACTAAATAACTTTCCCGGTCAGGGATGTACCTTCAAATCCCAGGAAGAATCTATGGAGAGGAGGCAGGTTCCCACAGCAGCCATCCTAGGATGGAGAGACCTCAAGGGCAAGTGTGAAAAAGTAAAGGGTAATCCTAGATATTATCCCTGGCTTCTCTCCACTCCTCACTCCAGAAGCAAGGTATCTGGATTATTATGATTTATCCCCCGAGACACCAATATCTGGCTTCTACCAGAAGGATAAGCAGGGACCATCCCCACAATAGCAGGCAAGTACAAGGCTTGAATAGCTTTGCTGTATAAATCACCCATCAGGTACGGCACATTGCCCTGCCACAAGGTGCTGCCACACCCCACAGACCCATTCACTGCTCGCTCTTGCTCTCTCTCATGCTCTCTCTCATGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCCCCTACACCTCCATCTCTGTCCTGAGGAGCCACCAAGGTACTTCGCATCACCATAGATATTCTAGACTTTTATGAAAAGTATAGTAGGCTCTTATTAACCTTTCTGAGGCTCTGCCAATTGCAGATTCACGCACAAGTGACAAGCGTGTCAGCCATGGTCCTCATAGTCCTGGCTGTCCCATGCACGGAGGGTGAGGACTGATGATAAGAACTCTTAGATTTTCAATACTCTCACATACTTCCTTATCCTGTAGGGCTGCTGTAAACATCTCTGGGCATTATGCACAGTACCTAAAATTCATATGGAAATGCAAGATTCAGGATAGCAAAACATTTTCTGAAAAGAGGAAACAGGTAGGAAAATTCATATTCCTGATATCAAAACATGCTGTAAGCCAAGTATGACACTCCTTAAGGACAAACTGAGTATACAGGGCAGAAGGGACAGTCCAGACTAACCACATATCTATTGCTAAGTGGTTATGACGAGGGGACCAAGACCACACCACAAGGAATGGACGGTCTCCTCAACAAGCAGTTGAGTCCCAGTCCAGACCCAGTCAGCACTGTTAGCATCCTGCACCAGTGTCTAACAACAGGAGGAAGACAGGTTTGCCACTGCTGTCCTTGTGTATCATCAGGGGATGCAGCCTGCAGTGCCAGCAGGCCTCCCTGGCCCGGAAGCTGACAGTCTTTCCTGTTTCCAG
Seq C2 exon
GTACCCCTGGCAGCTGTTCAGAAGACACCTGTCAGAATGGAGGCACCTGTGTCCCAGGTGCCAATGCCCACAGCTGTGACTGCAGGCCTGGGTTCAAAGGCAGACACTGTGAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:27
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=0.150
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]