MmuINT0133905 @ mm9
Intron Retention
Gene
ENSMUSG00000020696 | Rffl
Description
ring finger and FYVE like domain containing protein [Source:MGI Symbol;Acc:MGI:1914588]
Coordinates
chr11:82624530-82626312:-
Coord C1 exon
chr11:82625902-82626312
Coord A exon
chr11:82624614-82625901
Coord C2 exon
chr11:82624530-82624613
Length
1288 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
GCACCTTTCTCTTCCCACAGGCC
3' ss Score
12.29
Exon sequences
Seq C1 exon
CAGACCTGCTTGGACTGTAAGAAAAACTTCTGCATGACTTGTTCGAGCCAAGAGGGGAATGGGCCACGCCTCTGCCTTCTCTGCCTACGGTTCCGAGCCACGGCCTTCCAGCGGGAGGAGCTCATGAAGATGAAGGTGAAGGACCTGAGGGACTATCTCAGCCTCCACGACATCTCTACGGAAATGTGCCGGGAGAAAGAGGAGCTGGTGTTCCTGGTGCTTGGCCAGCAGCCTGTAATTTCTGAGGCGGACAGGACTCGTGTTCCCCACTTGCCCCAGGCCTTCCCTGAGCAGCAGGCCTTCCTGACCCAGCCTCAAACCAGCACAGTGCCTCCTACCTCACCTGGCCTCCCTTCTTCACCTGCACAAGTCACCTCTGTCCCCTTAGCCCAGGATCAGGAAACTCAGCAG
Seq A exon
GTAGGAACCACCACGCAGCCTCTTCACCGCTGTGTCTGCTCTGGGACTCTTTTTATTCCCTCCGCTGCATTGTGGGAGTGGGGTGTCAGGTGTCATGTCTAGATGGTGTAAAACCTTTCTGCTTGTTGATTCTAGAAGTGGTGTTTTCTGATCATTAGGCTCAAGCTCTGACTTCAGGGAAGGTAGGCCTAGTAGTACTGTGTTTTTGTGCAGTTTGTTTGTGATACCTTCATCCCCTAATTAGACTTAAAAAAATCTTCTTTTCATTGCTTCAGAAATACTTTGAGGAAAATCATTCTCATCTCTAGTTTGCCCTTCAGTTTGCTGCCCTTTTGACTGATCTAAGTGGCAGGAGAGGAGAGCAATGGGGAGCATTGGGGAGGGCGGGCCTTGCCGCTGTCCTGCATACCATGTGCGAACAGAACAGCGGTGGCCAGCATGCTGTGGGGCTGTACCCTGCCTCCCTGTTACATAGTGTTGCCTGGAAACGGTAAGCCAGGAGCAGCCAGTTGGGTTGTGGGGAGTCCACAGTCAACACGTACCGTCTCCACCCTCGGGAAGCCCTGACAGAGAAAGGCTAAGCACGAGACCCGCTCTGAGGTTTGTCTGGGGTTTGTCAGGAGTGGTGGTGTCACAAAGATCTGCAGAAGTCTCTCACTCATTCTGCAAGTCACAGGGCTTGGGCACAGAAAGATTAGGACCTAGATCTCTATCCACTGTCATCGTCCCCCCTCCCTCCCCCCTTTGCACTGTCCTGAAACTCACTCTGTAGATCACACCAGGCTGACCTCAAACTCAGAGATCCACCTGCCTCTGCCTCCTGGGGCAGAGTGCTGGGCTTAAAGGCGTGTCCCCACCACGGGCATGAATGAGGTGTTTGAACAAACTAGTGGACACTGGTGCAGAGGCAGAACCGTGGGAGTGGGTGGAGGCTGTGGGGAGGGCATTGGGTTAAGACAGTCTGCTGGAGAGACACCTTTCACCTCAACTGTCCAGGCTGAGCACAGACTGGTGATGCGTGGCGGCTAATGCCACCCTCACTGCTGGGCAAAATTAGCACACTCTTGTACTTGATGCAGCTTTCCATCTGGTGAACTCTGTGTGTATCATCTCTGGCTGTGAGATTCGGCTGTTAGACAGCAGGCATTCGTGGTCCTCCTTCGGGAGCCTTGTTTCTGGAGGGAGACGGGAATACACTTTTGGACATTCGTGTGAACTGAGAGCGGCCCATGGTTTGTAAGTCACTGGGCATCTCTGTGGCTGTGATGGCACCTTTCTCTTCCCACAG
Seq C2 exon
GCCGTTGGCCATGTGTCTCAGGACCACGAGGAGCCCATCTTCCCGGAGAGCACAGCCAGAGTACCTACTGAGGATGAGACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020696-Rffl:NM_001164569:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.372 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0136316=FYVE=PD(73.3=46.0),PF102084=Armet=WD(100=55.5),PF0203722=SAP=WD(100=15.3)
A:
NA
C2:
PF102084=Armet=PU(26.5=96.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAGGACCTGAGGGACTA
R:
AGGTACTCTGGCTGTGCTCTC
Band lengths:
343-1631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: