RnoINT0146335 @ rn6
Intron Retention
Gene
ENSRNOG00000033110 | Svep1
Description
sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [Source:RGD Symbol;Acc:1588987]
Coordinates
chr5:75190570-75191815:-
Coord C1 exon
chr5:75191645-75191815
Coord A exon
chr5:75190744-75191644
Coord C2 exon
chr5:75190570-75190743
Length
901 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGC
5' ss Score
6.06
3' ss Seq
AACTTGCTGCCCTGTTCCAGGCA
3' ss Score
7.45
Exon sequences
Seq C1 exon
ATTGCCCATCTTTAGAAGGGTCCGTGCCTCACCTGAGACCTGCATCAGGAGATCGAAAGCCAGGTTCCAAAGTCAGTCTGTTCTGTGACCCGGGCTTCCAGATGGTCGGGAATCCGGTGCAGTATTGTTTGAACCAAGGGCAGTGGTCACAGCCACTCCCTCACTGTGAAC
Seq A exon
GTGAGCAACCTTTGTCCAACTCGGGGATTGCTAGACAGATGCTCGTCAGATACTGCCACAAACCCAGCAGACGTCCAGTCTGTGCCCTGGCCCTAAGAGACTGAGCCAGGCACCATGGGGGAGGTGGGTGATGGGGGTACAAAAAAGACTCCTGACAAATGCCTCTGAGGTGCTGGCAAGGAACTCAAAACAGGTGAAATAAGGTCCCTTTAGGGTAGACAGCCACCCTGAGGTACGCCATTGCTGGATGAGGAAAGAGGGACAGGTGTCTCGAGCAGGATGTCCCAATCATTCATTAACTCTACAAGATTTAGCTGCACACTGATACATATTCTAAAGATGCTGGCCCCATTCTTGTGTTTACATTCTGGAGGAAGAGATGGGGGAGAGGGGATGTATATAATAAGGCTTGTTTATAACGAGTAAAATGGTGAAGACCAGAAAGACCCTAAGCAAGTAGCAAGGGCAGGAGGTGAGGAGATTTGTAGAGACAAGACACTGCCAAAAATAGACAGTAGCACCTGACACAGAATCTATTTATCTTCTGGTCTGTCCACCTCACTGGACAGGAAGCACCACAAAGCAGGAGTCCCATCCATTCCATTCACTGCTGTAAGCCCAGCACCTAGGACAGGGCGTAATGGGTGGTAAGAGTACCACAGATGTTTTTGAATGAATGAATGGATGGATGGGTGAATGAATGAATGACATGCCTACCGTGAACCAGACAATGTGCCACATGCTGAGAGCACATGTGTGGCAAGCAGTGTAGAACACTCTAGTTACTAATGTTTGTGCACCGTAGGGAAAGGGTAGCTACCTAAGGCAGCCACCATGGAAGTAGGTCCATGCAAGCAAGATGCTCTTTGAGCACTTTGCACAACTTGCTGCCCTGTTCCAG
Seq C2 exon
GCATTCGCTGTGGGCTGCCTCCCACCTTGGAGAATGGCTTCTATTCAGCCGAGGACCTCCATGCTGGCAGCACAGTGACCTATCAGTGCACCAGTGGCTACTACCTGTTGGGTGACTCCAGAATGTTCTGTACGGACAACGGGAGCTGGAACGGCATTTCTCCATCCTGTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033110:ENSRNOT00000047200:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PD(94.8=94.8)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTTAGAAGGGTCCGTGCCT
R:
GACAGGATGGAGAAATGCCGT
Band lengths:
334-1235
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]