RnoINT0113534 @ rn6
Intron Retention
Gene
ENSRNOG00000017223 | Plg
Description
plasminogen [Source:RGD Symbol;Acc:619893]
Coordinates
chr1:48552038-48553851:-
Coord C1 exon
chr1:48553737-48553851
Coord A exon
chr1:48552178-48553736
Coord C2 exon
chr1:48552038-48552177
Length
1559 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
ATTTCTTTTCCGTCTTGCAGATA
3' ss Score
12.57
Exon sequences
Seq C1 exon
TGTATCTGTCAGAGTGTAAGACTGGCATCGGCAAGGGCTACAGAGGAACCATGTCCAAGACAAAGACTGGTGTTACCTGTCAAAAGTGGAGTGACACGTCCCCCCACGTACCCAA
Seq A exon
GTAAGCGCTGCTATTTCATGTTGGTGTTCATGAGTGTATTCAGAACAGTTCCGCTGTTTCCAAATTCCACTGCCTGGTAGTGTGAGCAGAGACCCTTTTGGTGTGGATTCTGGGCAGCTGAATATTCACAATGCAGAAGGGAAAAAATGGTTGGTTTCTATTAATCTCATTATATAATATCTGAGAAGTCTTAAAACATAGTAGGAGGCATGTCAAAAGAACCACTGAATTTTAGGTTGTCCTAGTTTTCATTCTGTTCCTGTGATAAAAATATTGTGGCAAAAAAGTAACTCAGGGAGAAAGGGAATTTACTTTAGATGACAATTAATGACAAATTACAGTCTGTTATTATGGAAAAGTTACAGCAGCAATAGCTTGACCCTGCGAGTGACAGGGAACAAGTGCATGCATGCTTATTGGTGCTCAGCTCCTCTGTACTTACACACTCCAGGATCTCCTACATAGGGAATGGTGATGCCCACTGTGGGCCGGATCTTCCCACATATATTAATGTAATGAGATAATACCCTCACAGGGCTGCACACAGGCATCAAGAGATTTTTTCACTGAGATTCTTTTCTTAGGTGAGTCTAGTTCACGGCATGTTGACAGTCACACAACTGTAACAGAGACCAAGTATCAGAAAATGATGCTCGTTTAGAGATGGGTGTGTCTCGGTTGAATGCCAGGTTGGAGCCTGCACAGCGTGCCCTCCACCTCACCACTGTGACCCGATGAGGATATAAACCATGAAAAACAAATAGGAACTTTGCAGCTTGTGTGTTATTGTAGGGTCATTCTGTGTGTGTCCCCCACCATAGCATTAAGTTGGGTTCTCTATGATGACTCCAGGGGCCACACTCTTTCATGAACTAGCTAAGCTTCTAATCTGGTAGACGGCCCCCCAAACCGGGACATGGAGGAGCCAGAAATTAAGCTTGCCTTTTCAAACTGCAAGTTCTTGCATGTTTTATCTAGCTATCTTTGCAGTAGCTCATTTCCAGAGCAGAAGATGAGCTCCGCTTTCCCCAACCTTGATCACGTAGGCTGCGTTTCAAAGAAAACTCGGCCAGTCTCTGCGATTACACAATAGACTTCAGAGCCTTCACCCGCTGCTGGCTGTTAGCCTCCATCTGCTTTTCTCCTGTTTCACTACACAAGGCTCTCCCATCAGTAACAGGTTTTCTTTTCATTAAGAGCAAGTGACAGAATGTAGAAGGTTTCAGCAGAAGGCTAGGGGCGGAGGTCACACAGACAGAAGAGCGATCGGTGCTGTGGATGTGTGGGGAGGACCACTGGCCTCCGAGGTGCTGGCGTTCTCCTGCCTGCTCAGTATACATTCTTTGGTTAGACCCAAGACTTAGCTGCCCCAAGAGTAATGACGGCAGAGTGAGCTGTGTGACACGAGCCTTCCCATCCATAGATAAAGGAGTGACAACCAGCAGCTGAAACACGTTCAATGACAGAACCAAGCCCTCAGTATGAGGCACAGCATCTCCTACTTCGCTAGTGCGCCGTTCTGCATGACGTGCTCACCACATTTCTTTTCCGTCTTGCAG
Seq C2 exon
ATACTCCCCCAGCACACACCCCAGCGAGGGACTAGAGGAGAACTACTGTAGGAACCCAGACAATGATGAACAAGGGCCCTGGTGCTACACAACAGACCCGGACCAGAGATATGAGTACTGCAACATCCCCGAATGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017223:ENSRNOT00000023368:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.058 A=NA C2=0.276
Domain overlap (PFAM):
C1:
PF0002421=PAN_1=PD(1.3=2.6),PF0005113=Kringle=PU(41.8=84.6)
A:
NA
C2:
PF0005113=Kringle=PD(57.0=93.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATCTGTCAGAGTGTAAGACTGGC
R:
CTTCGCATTCGGGGATGTTGC
Band lengths:
254-1813
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]