RnoINT0146348 @ 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
chr5:75156114-75157597:-
Coord C1 exon
chr5:75157424-75157597
Coord A exon
chr5:75156291-75157423
Coord C2 exon
chr5:75156114-75156290
Length
1133 bp
Sequences
Splice sites
5' ss Seq
AACGTGTGT
5' ss Score
3.87
3' ss Seq
ATCTGACTCATCTTTTACAGCAA
3' ss Score
7.65
Exon sequences
Seq C1 exon
AGAGCAGATGTGAGGCTCCGGCTGAGTTTCCCAATGGGAAGGCTGTCTTGGAAAACACCACATCTGGACCCAGCCTGCTGTTTTCCTGTCACAGAGGCTACACCCTGGAAGGGCCCCCTGAGGCACACTGCACTGCAAATGGAACCTGGAGTCACCTGGCTCCCCTCTGCAAAC
Seq A exon
GTGTGTGTTGACTTTAGGGGGTGTTTTAATCACATTCTGCCCCACAGCTAGTTTCATACATATCTCTGCTTGAAGGGGAAATACTGATAAATGAGATCAGTCCCGGGAAGGCCGTCTGTGGCCATCAGACCCAACTTTATGGGATATTTTAGAACTCTACTTACGATATATTATAACAGCCTGTCTACGAGTCAGCTTTTATCAGATTCCTCTGCTGATTAAATTCAAGCATTAATAGAAATTACAAATTAATGAAAGCATTTTGAAACGAAGATATTGTGAGTTCCAGTGACACGAAGAAAGGGGGAGAAAGAAAGAAGATACGGTTAAAATCTAATGTTAATATATAACATATAAATGCGGTAAATAAGGATAATTTGACCACTTGAATGAAAACCATACAAATGGAATACAGCGTGAGAAGGCTTCTGACTAGTGTGTAAAGTACTGTAGTGCGTGAACACAGCCTTCAGAATTCAGAAGAGCCCTACCTCAGCAAAACTTACTTTCCACTTAAAATCAGAACAACCGAAATAGCTTGAAGCCTGTGTCCGTATGTGTGGCATACTTTTGCTCTGAGCAAAGTCGAGCCCTAGCGACACGTCCTGTGCTTCCTTCTAAGCTGTGGAAACATCCTGTTTTTACCATCAGGCCCACAAATACAGCATGAGGTCCTGTCATTCTGTTCCTCACAGTGCAGGCCTGAAGTCAGGCTCACCCTGCACGGCCAGGTCTGATGCTTCTCTACTCCCGTCCTCCCTGAAGCATGTTCAGTAAGAGGATGGAGTTCAACAGAATTCACCATGCTGTTGACACTCATCAAATATTGAGAGACAGTGTGGCCCTTGGTTTCTTATATGCCTGATATTTAATCTTCACAAATAATTTTATGTGGGTGGAAAGCAAATCTGGGCTGATGCCTGAAGTTCTAAATCGTGAAACCCTTTGCTGGGCGTGGTGGGACTGAGTCAGGAGGGCAGGAGTTTGAGGCCAGAGTACTCCATTTTCGTCTTAAAATTTATATTATTATTGTCATTGAAGACCCATGCTCTGTAGGCCTCTACTTTGTCTTCAAAGAGATAAATTAGAGAATGAGAAGACAGCTCAGTAAACATCTGACTCATCTTTTACAG
Seq C2 exon
CAAATCCATGCCCTGTTCCTTTTGTGATTCCTGAGAATGCCCTCCTTTCTGAGAGAGAGTTTTACGTCAACCAGAATGTATCTATCAAGTGCAGAGAAGGCTTCCTGCTCAAAGGCAACGGCATCATCACGTGCAACCCTGACGAGACTTGGACACAGACAAACGCCAGATGTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033110:ENSRNOT00000047200:42
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.7)
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:
GAGCAGATGTGAGGCTCCGG
R:
ATCTGGCGTTTGTCTGTGTCC
Band lengths:
344-1477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]