RnoINT0069119 @ rn6
Intron Retention
Gene
ENSRNOG00000022321 | Hapln3
Description
hyaluronan and proteoglycan link protein 3 [Source:RGD Symbol;Acc:1308098]
Coordinates
chr1:140827295-140828753:-
Coord C1 exon
chr1:140828451-140828753
Coord A exon
chr1:140827756-140828450
Coord C2 exon
chr1:140827295-140827755
Length
695 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
AATGCTCCCCTTTCCCACAGGGC
3' ss Score
12.21
Exon sequences
Seq C1 exon
GTGTGGTTTTTCCCTACCAGCCCCGAGAAGGGCGCTACCAGCTCAATTTCCATGAGGCCCAACAGGTCTGCCAGGAGCAGGATGCTGTGGTAGCCACTTTTGAGCAGCTTTTCCGAGCGTGGGAGGAAGGCCTAGACTGGTGCAATGCAGGCTGGCTACAGGATGCCTCCGTGCAGTACCCTATAGTGCTGCCCCGGCAGCCCTGTGGAGGCCTGGGTCTGGCACCTGGGGTTCGCAGCTACGGCCAGCGCCATCACCGCCTGCATCGCTATGACGTGTTCTGCTTTGCTGCTGCCCTCAAGG
Seq A exon
GTGAGTGGAACAGCCAGGCACAGGCCTGCCCTGCTTGACAGTTACCTGAGGGAGAGCCTATGGAGCTTCTAGAACCGTCTGCCCTTCTCTACCTGCCTGACCTGGCCTGAGGTCTGAAGTGTTAACAGTTCTGGAGGCAACGTGTCCTACAGTTCTCAGTGCTTTGCCCTGATGCTCCACGGCCTTCATTGGCTATATATTCATCAGACATCTTTGGAGTGTCTACTCTGTGTTGGGCTGTGGGTCAGCACAGACAAACCACATCTTTCCTGAAACACCATCCTTGTCATTCACTGCAAGGTAAAGGAAAACAGAAGGTTATTCAGTGCTGCATTGTGTAATCTCAGCCCTTGGGAGGAGGAGGAGGCAGGAGGATCAGAAGTTCAAGTTCAAGGTCCTCCTCCGCTACTTAGTTTAAAAAGTGTCTGCTGCCATGTAGTAGGTGCTTAGAAAAAGGCAAGTGAGAGACTGGTTCAGTCTGGTTGGGTGCCCCCTCAGAATGCCATTGGGGTGTACAGAAATGACTAGAGCAAACCCAGCCCTGTGGCAGGTGTGATGGTGGGTTGAGGGCTGCAAAGGTGGGCCTTCAAAGTGTCCGACACAGATTCTCATAAGGCAGTGAGTGCCTCACTGCCTGTGGCAGGTTCTTCTGCTTCCTATGCTGTGTAGTACTCAAATGCTCCCCTTTCCCACAG
Seq C2 exon
GGCGAGTGTACTACCTGGAGAACCCTGAGAAACTGACGCTGCTGGAGGCCAGGGAGGCCTGTCAGGAAGATGGTGCGCAGATCTCTACGGTGGGTCAGCTCTTTGCTGCTTGGAAGTTCCGTGGCCTGGATCGTTGTGATGCTGGCTGGCTGGCAGACGGAAGTGCCCGCTACCCCATCATTCACCCCCGACCCAACTGCGGCCCACCTGAACCTGGAGTACGAACCTTTGGCTTCCCAGACCCCAACACCCGCTACGGTGTCTACTGTTACCACCAGCACTAGCAGAGTGACAAGCTGTATATCTGCCCTGCCCCTAACTTTCGGGACTTAGTGTTTATCAGGTGGACCATTGTCCCTTGTGGGTTGGGGAACTTCTTGGATTGTTTTTATACTTCCCAACTTAAACATTTAAAGTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022321:ENSRNOT00000032174:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.053
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
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:
GCTCAATTTCCATGAGGCCCA
R:
CGTAGAGATCTGCGCACCATC
Band lengths:
352-1047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]