RnoINT0118639 @ rn6
Intron Retention
Gene
ENSRNOG00000000433 | Prrt1
Description
proline-rich transmembrane protein 1 [Source:RGD Symbol;Acc:1359348]
Coordinates
chr20:4392626-4394265:+
Coord C1 exon
chr20:4392626-4392765
Coord A exon
chr20:4392766-4393726
Coord C2 exon
chr20:4393727-4394265
Length
961 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTCGGCTTTTCCATGGCCAGGCC
3' ss Score
6.13
Exon sequences
Seq C1 exon
CTCGCTGCTGCTGCTGCTACCGCCGCTGCACCGGCTGCGCCATCCGGGACTCAGACTCCTGCGCCAGCAGTCAGGGGGCCCTGACTCTAGCTTCAGAGACCCTGTTCCAGCGCTTGCGAGCATGTCGTCAGAAAAGTCAG
Seq A exon
GTAAAAAAAACTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTCCCCACCCCTATCAACCCCTACCTAACCCCCACTTGCCCCAGTCCCCTTCTTTGACCCCCTCTGGGTGTAGTGTGTGGCTCAGTTCCATTCCCCTTCTCTCCGTGCATACCCCCCACCCCTCCCCTTTCTATATTCCATCCTCCTTCCTTAGGGTCAGTCTGCCTCCGTCCCTTGTCAACAACATTGGTGGGGGGGGCAGTTTAGAAAAGGAAAGGGAGGCACAGTCAGGTACTGCAGGGACAACATCCCTGGGGGTGACAGATGGACAGTCACCGGTTCACTGGCATGGAGACACCCAGTGGAAAAATTACGGAGACTTGATCAGACGGGGTTGTTGGGAAAGTAGTATCTAGAAGATTCCTCTTTATTGAGATGAGATTTCCCTATGTAGCCCAGGCGGGTCTTGAACTTCCTCCTGTTCTTCACCCTTCTGCCTCTGCTTCACAAATACTAGGATTGAAGGCATGAGCCACCATGCCTAGCCCCAGGAGCTCTGTTATGGGCCTTAACCGAGGCCATGAGATCCCCAGGTAACTCCGACCTGACGCAAAGCGGAAATGTTAAACTGAGCGTTCATGCCCCTGTGACACGGCCACATGTGCTGGGAGAGGAGCAGCTCAGACGGCCCTGGAAGAGGGTTGTGGTTGACAGCAGGGGAACCTGGGAGGAGTTGTGACAGTTGTGACGGCAAAACTAGAACTGGGGCCAGGTGGCCTAGATACAACCCCTTCCCTGACCCCAAAATGGGAGATGTCGTCTCAGCTATCTCTCCCTCGCTATTTCTCCATCTCTTGCTGTCTCATGTCTCTTACCCTTCTGATCTCTGCTGTCTTCTCTCTCCCCTTATTCTCTCCTCGGCTTTTCCATGGCCAG
Seq C2 exon
GCCTTCCAGACTCGGTTCCCCACACTTCACCTCCGCCCTACAATGCCCCCCAACCTCCAGCCGAGCCCCCCATCCCTCCCCCACAAACCGCTCCATCCTCTCATCATCATCACCACCACCACTACCACCAGTCTGGCACTGCCACCCTCCCGCGCTTAGGAGCAGGTGGCCTGGCCTCTGCTGCGGCTGGCGCTCAACGTGGTCCTTCGTCCTCTGCCACGCTACCGCGGCCCCCCCACCATGCCCCTCCCGGTCCCGCTGCTGGGGCTCCCCCACCCGGCTGTGCTACCCTACCCCGCATGCCACCCGACCCTTATCTGCAGGAGACTCGCTTCGAGGGTCCACTTCCCCCACCACCGCCTGCGGCCGCCGCCCCACCCCCACCAGCGCCTGCCCCGACGGCCCAAGCCCCAGGCTTCGTGGTGCCCACGCACGCGGGGGCGGTGGGCACGTTGCCGCTGGGGGGCTACGTGGCTCCGGGCTACCCGCTGCAGCTGCAGCCGTGCACCGCTTATGTCCCGGTGTATCCGGTGGGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000433:ENSRNOT00000000495:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.800
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
CGAGCATGTCGTCAGAAAAGT
R:
TCTCCTGCAGATAAGGGTCGG
Band lengths:
351-1312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]