RnoINT0069121 @ rn6
Intron Retention
Gene
ENSRNOG00000049949 | Hapln4
Description
hyaluronan and proteoglycan link protein 4 [Source:RGD Symbol;Acc:1308408]
Coordinates
chr16:21087785-21088591:-
Coord C1 exon
chr16:21088471-21088591
Coord A exon
chr16:21088148-21088470
Coord C2 exon
chr16:21087785-21088147
Length
323 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CCTGATTGGTCGCCCCACAGAGG
3' ss Score
6.8
Exon sequences
Seq C1 exon
GCGTGTGCTCCAGGAGCCCTCGGTCACCGCGCACTCTGGGCCGTGGCCTGGGGACTCCTGCTGCTGGTCCCCGTGCTCGCAGGGGCGCAGCGTGGCAGGAAGAAAGTCGTGCACGTGCTGG
Seq A exon
GTGAGTTTTGTGCGAAGCTGTGGTCATCCCCTCCAACCCCCAGTACACACACACACACACACACACACACACACAGACACACACACTCACACACACACACACACACACACACACACACACGGGTGCGCGCGCGCATGCACGCACGCACACACAGCACACACACATCGGAGGCCTAGAGTGAACGACGGGAGTGGGATGGGGTGGAGGATTGCCGTGGTCCCGACACTCAGTCTCCTCTGAGCTCCTTTCCCACTGTAGACCTACATCCCCCTCCCTGGGTCCCTTCCTACCGCACCTTTGACCCCTGATTGGTCGCCCCACAG
Seq C2 exon
AGGGCGAGTCCGGTTCGGTGGTGGTGCAGACGGCGCCGGGGCAGGTGGTGAGCCACCGCGGTGGCACCATTGTCTTACCCTGCCGTTACCACTACGAGGCGGCCGCCCACGGTCACGACGGCGTTCGCCTCAAGTGGACGAAAGTAGTAGACCCTTTGGCTTTCGCCGATGTCTTCGTGGCTCTGGGTCCCCAGCATCGAGCCTTCGGTCCCTACCGAGGGCGGGCCGAGCTACAGAACGATGGACCCGGGGACGCCTCCCTGGTCCTCCGAAATGTCACCCTGCAGGACTACGGGCGCTACGAGTGCGAGGTCACCAATGAGTTGGAGGATGACGCCGGCATGGTAAAGCTGGATCTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000049949:ENSRNOT00000072565:2
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=0.033
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=95.9),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAGAAAGTCGTGCACGTG
R:
CTCATTGGTGACCTCGCACTC
Band lengths:
348-671
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]