RnoINT0118640 @ rn6
Intron Retention
Gene
ENSRNOG00000000433 | Prrt1
Description
proline-rich transmembrane protein 1 [Source:RGD Symbol;Acc:1359348]
Coordinates
chr20:4393727-4395046:+
Coord C1 exon
chr20:4393727-4394265
Coord A exon
chr20:4394266-4394860
Coord C2 exon
chr20:4394861-4395046
Length
595 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CCCCACTGTCCTTCCCACAGCCC
3' ss Score
10.48
Exon sequences
Seq C1 exon
GCCTTCCAGACTCGGTTCCCCACACTTCACCTCCGCCCTACAATGCCCCCCAACCTCCAGCCGAGCCCCCCATCCCTCCCCCACAAACCGCTCCATCCTCTCATCATCATCACCACCACCACTACCACCAGTCTGGCACTGCCACCCTCCCGCGCTTAGGAGCAGGTGGCCTGGCCTCTGCTGCGGCTGGCGCTCAACGTGGTCCTTCGTCCTCTGCCACGCTACCGCGGCCCCCCCACCATGCCCCTCCCGGTCCCGCTGCTGGGGCTCCCCCACCCGGCTGTGCTACCCTACCCCGCATGCCACCCGACCCTTATCTGCAGGAGACTCGCTTCGAGGGTCCACTTCCCCCACCACCGCCTGCGGCCGCCGCCCCACCCCCACCAGCGCCTGCCCCGACGGCCCAAGCCCCAGGCTTCGTGGTGCCCACGCACGCGGGGGCGGTGGGCACGTTGCCGCTGGGGGGCTACGTGGCTCCGGGCTACCCGCTGCAGCTGCAGCCGTGCACCGCTTATGTCCCGGTGTATCCGGTGGGCACG
Seq A exon
GTGAGTATGGGGCTGACAGGACCTAGGAGGACAGGGAGGCAGGTGCAACAGGGACGCACACACTCTGGAAGCTGGGAGAGAGTGAAACAGAACCAGGCTGTCCGCCCTTCTGGTAACAAACCCTGGACAGAAGAGTGGAGAGAGGAGAGACAATGGGTGGGAAAGTGGTGGACCTTGGGGGGAAGCGGGGAGGAGTCTGGGGGATCAAAGGTCAAGGTTTGGGCCGTGGTTCAGAAATCAGTTGGTCTGAAAGAAGGAAAACAGCTTGGAGGGAGAGAGAGAGATGGAACCTGGGAAGCCAGGGGTAAAAGAGGGCAGAAGCCTGGGCCTGGAGATGCTAAGGAAGATGGAAACAAGACCGGAAGGACAGACAGACCCATAAGCCATACCTTGTAGGACACTGTGGGAACTTCCCCGAATATTCAAGTTAATGATACGTGAAGAGAGGCCTAGGCCGATTTTACTGTCAGGAACGATTTTTTTTTCCCCTTAAGCAAAATCGTGTTTTTAAAAACCTCTTTGCCAATTGGCCAGCTGCTGGCAAGCAGCAAGACTGTTGGTGTGACGTCCCTTTCCCCCACTGTCCTTCCCACAG
Seq C2 exon
CCCTACGCAAGCGGGACCCCCGGGGGTCCAGGAGTGACCTCCACTCTGCCCCCGCCGCCCCAGGGCCCAGGGTTGGCTCTGTTGGAGCCCAGGCGCCCGCCGCATGACTACATGCCCATCGCTGTGCTGACCACCATCTGCTGCTTCTGGCCCACAGGCATCATCGCCATCTTCAAGGCCGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000433:ENSRNOT00000000495:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.800 A=NA C2=0.403
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF045057=Dispanin=PU(54.4=79.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGACCCTTATCTGCAGGAGA
R:
CATGTAGTCATGCGGCGGG
Band lengths:
347-942
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]