RnoINT0102733 @ rn6
Intron Retention
Gene
ENSRNOG00000052873 | Npnt
Description
nephronectin [Source:MGI Symbol;Acc:MGI:2148811]
Coordinates
chr2:238027206-238028685:-
Coord C1 exon
chr2:238028566-238028685
Coord A exon
chr2:238027341-238028565
Coord C2 exon
chr2:238027206-238027340
Length
1225 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TTCATAAGATTGTGTTTTAGATA
3' ss Score
6.03
Exon sequences
Seq C1 exon
GTGCTCTCTCGTGTTCCATGGCAAACTGTCAGTATGGCTGTGATGTGATCAAAGGCCAAATCCGATGCCAATGTCCTTCCCCTGGCCTGCAGCTAGCTCCTGATGGGAGGACCTGTGTGG
Seq A exon
GTGAGTGCACTCATGAAGCATCTGTCAGGAGATACTGTGGGGCTGAGCAGATCACCAAGGCTATGCCATTACGTGTGTTGTACCACAGGGCATACTTAGCGTTCCCCTAGAGCATTAAGATCGCAGCTTAGATTATGGCAGAGTTTGGACTTTCTAAGCCTGGCTGAGCTGCAGACTAGCTATGTAAACTTAGGAAAAGAACTACTCCTCTTGGAGCTTGGGTCCCCCTTTTCTTGCAATGTAAATAATAGTACACAAAACCATTACAGTGGTGAATGAGATCATGTGTTCCGAGTTCAGAAGAGCTCGCCGGAGTCTCCTGCATGGAGCTATTCACATTAAGACCCATTTGTTAAGTCGTTGCTTTATTCAAGACTCTGTTAAGGGCTGGCTGCATAGCAGTGGGCAAAGCACATGAGGTTTTGGTCCATAAGAAGTTGACCTCCTAGTGGGGAAGACGGAAAATAAATAATACTCAATAAAATGACTGGCCTAGCTAAGTGCTAGCAGAAGGTAGGAAGAGAAACAAAACTAAAAGGCCTGTCTAAGAAAATCATCCTTAGGGAATTCCTAAAGTTAGACCGGGGCTATTAGCTATAGAAAGAACGTGCCAAGGGACGGGAGAGGCAGCCGGCTAAGAGCATGGGCTTCCAGGATTCCCAGCACTGACAAAGCACATCATAGCCATCTGCAACTCCAGTTCTAGGGGGATCCTACTGTCTCTGGCCTCCTTAAGCACAAGACAGGCACGTGGTGCACACATCTACGTGCAGTCAAAGCAGTCATACAGAGGAAATTTAAAATAAATTTAAGGAGCCTGTGGAGAGGTGAAGTGACTGGAGGAGATAAGATTGGCAGCCCAGTTTGAAGACTTGTTTGAGTCTGAGTTGGGGGATACTGAGTAGGAATGGGACGGTGGAAGATGCTAGACGATTCCAGCAATCTTTCAGAGGTAGAAATAGCAGGACTTCGTGGTGGTTTAGGAGTTGTTGGCAAGAGGCTTAGCACGCAGGCTTCCAGTTCAAGCAACTGAGTAGACGGCGTTACATCTACTGCTGCTGGCTGTGAGAACAGACGAGTTCAGCTGAGGAGGGTGAGGTGAAAGCTGGAGGTGTGGAATTTTTTGTTTGGGGGACGTTCGGATGTGGAATGTGTTGCAGGGGTAGCGGGGGATCCCAGTTTTGATGAGCGCCCGTGCTTTGCTCTTCATAAGATTGTGTTTTAG
Seq C2 exon
ATATCGACGAGTGTGCGACTGGAAGAGTCTCCTGCCCCCGGTTTAGGCAGTGCGTCAACACGTTTGGGAGCTACATCTGCAAGTGTCACACTGGTTTCGACCTCATGTACATTGGAGGCAAATATCAATGTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052873:ENSRNOT00000079479:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=PD(8.9=9.8),PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.7),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTCTCTCGTGTTCCATGG
R:
CGTGACATTGATATTTGCCTCCA
Band lengths:
255-1480
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]