RnoINT0118641 @ rn6
Intron Retention
Gene
ENSRNOG00000000433 | Prrt1
Description
proline-rich transmembrane protein 1 [Source:RGD Symbol;Acc:1359348]
Coordinates
chr20:4394861-4396243:+
Coord C1 exon
chr20:4394861-4395046
Coord A exon
chr20:4395047-4395187
Coord C2 exon
chr20:4395188-4396243
Length
141 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
3' ss Seq
CCCTCGCCCCTCCCCGGTAGGTG
3' ss Score
10.04
Exon sequences
Seq C1 exon
CCCTACGCAAGCGGGACCCCCGGGGGTCCAGGAGTGACCTCCACTCTGCCCCCGCCGCCCCAGGGCCCAGGGTTGGCTCTGTTGGAGCCCAGGCGCCCGCCGCATGACTACATGCCCATCGCTGTGCTGACCACCATCTGCTGCTTCTGGCCCACAGGCATCATCGCCATCTTCAAGGCCGTGCAG
Seq A exon
GTGTGGGTCGGGGGCGGGAAGTAAAAGCTTAGGCTGACCAGGGGCTTCCTTAGACCGGAGCATTCTGGACATAGTCTTAGAGGGGGGCTGTGGCGGGTGAGCAGTGGCTCTCTGACCCCTCCCCTCGCCCCTCCCCGGTAG
Seq C2 exon
GTGCGCACGGCCTTGGCCCGCGGAGACTTGGTGTCCGCCGAGATCGCTTCGCGCGAGGCCCGGAATTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCAGCTATGGTGCTTTGTACCATCCTCACTGTAGTCATCATCATTGCCGCCCAGCACCACGAAAACTACTGGGATCCCTAAAAACGTCCCCGTCTCGGCCCCGCTCCGTGCCCCCTCCCAACCTCCCAGGCGCGTGGCGCAGTCCTGCCGCCTACCCAGAGCGCGCCCTGCACATCCTCCTGAGGCGCCGCTGGACTTCCAGACATCATAAACTCCGCCCCCACGGAACCTCTGGCCCAGAGAGTACGCTCAGTTCCTCAGGAACCCCTCTAGCACCCACATCCTCAGCGGCACTGGAATCCGCGCCAAACCCCGACCCTCCAGTCGCCCCAATTCCCCACCCCATCAAAGTGCAGTGCCAGCCAGGGGCGGATCTCTCCTGCTCTCCGCTCCCCAGTAGGGAGTCAGGTCCCAGAAGCTCCGCCTCATCTATAAGCTCCGCCCCAAATCCCACAAACCCCGCCTCCAGGTCGGCAGGCTCCGCCTTCTTTTCTTCTTTGGGGTTTTTCAGTCTGGTGATTGGGTCTGTGAATCCAGGCCCCCAGCCCACAATACAGACGGACTAGTCCCCCTACCTCCCTAAAAGGACTCAGCCCTGGGAGAACTACACCCCCACTCTAGCTCGGATTTTTGCCAGTGCGGATTTTTCTCCCCGCCCCCAACCCCCATCTCTGCCTATTTTCTTGCTAATTACAGAACTTCCCATTTTGCGGCTTTTGGAGTGAGATGAGGCAAGTTCCAGGTTTAGTACCCCTCACTCTGGAAAGAGAACCAAGTCCCTATAATGTAAATACCCTTTCTACATGTGCCAACCCCTGGGCAGCGGGGGCAGAAGAGAATCCAGGGTTAAAGGGAGGGAGTCGACGCTCCCCCGCTCCCCTCTGCCCTAGACTTGTTTTGATCTGTGTGTGCCAGTGTGTGTGAACTTCTGAAAGACAGTATTAAAGACATTTTAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000433:ENSRNOT00000000495:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.403 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF045057=Dispanin=PU(54.4=79.0)
A:
NA
C2:
PF045057=Dispanin=PD(43.3=66.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTACATGCCCATCGCTGTG
R:
AGTAGTTTTCGTGGTGCTGGG
Band lengths:
247-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]