RnoINT0076716 @ rn6
Intron Retention
Gene
ENSRNOG00000001804 | Itpr2
Description
inositol 1,4,5-trisphosphate receptor, type 2 [Source:RGD Symbol;Acc:69649]
Coordinates
chr4:180549053-180550847:-
Coord C1 exon
chr4:180550664-180550847
Coord A exon
chr4:180549310-180550663
Coord C2 exon
chr4:180549053-180549309
Length
1354 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
AACCACTTCTTGCCTTTCAGTGA
3' ss Score
7.83
Exon sequences
Seq C1 exon
AATTCTTTCTACCAGCAGTTGCATGAACAAAAAAAGTCAGAGAAATTCTTCAAAGTCCTTTACGATCGGATGAAGGCTGCTCAGAAAGAGATCAGATCCACGGTGACTGTCAACACCATAGACTTAGGGAGCAAGAAGAGAGAGGAGGACAGTGACCTCATGGCCTTGGGCCCTCGGATGAGAG
Seq A exon
GTGAGGGCCTTCCTGGGTACCTGCAGGGATGGCGTGAGAGAAAGAAGCACTAAAGCATTGGACTCTCATATAATTTTGTCATCATCATCTTGCTTCTTGGGGTTTAATTGCCCCCTCGAGTTTTCAGTATGGACCTCCATCTATAAAGGATTTTGGTCAAGGGATTGACTCTAAAAATAACCCTGCAGGACCAAACTAAATTGGAGTTTAATCAGTGTGGAAGCAACGGGCAGTGGGAAAGACATTGGAATTCTTTGTTCTGTGCAGTAAAGAAAACCATCCAGAGCTTTCTGAACACAGAAATTAATCTCTGAGGACAGAATTTATAGTGTTTGTATTAAAAATAACCAAATTATTGTCAGTTAAATACAAACTGTAGAGATGTTAGCATTCTACAATTTATCCTTTTTCCCATAAGATCTGTAGGAATTCTGTTCCCTCCGTGTGTGCCACACATGTGTGGGCTCTGCGGAGGCCAGAAGACGGTGTTGGACCGCCCTGAAGCTGGAATTATAGGAAGTTATGAGCAGCCTGACATGGTTCCTGGGAACTGAACTCAGGCCTCTGGAAGAGCAGCAAGGGCTCTTAACCACTAAGCTCTCTGTACTGGTTGGCTTTTGTTAATTTGATACATAGCTAGATCTAACAGGGAATGTTAATTGGGGAGATGTCCCCATAGGATTGGCCTGCAGACAAGCCTGTAGGGACATTTTCCTCTTCAGACTGAAGTGGAAGGGCCAAGCCTCTTGTGAATGTTGCCTCTGCTGGGTAGGTGGTCCTGGGTTCGATAAGAAAGTGAGCTGAGCAAGCCAGTAAGAAGCACTCCTCCATGGCCTTCGCTTCAGTTCCTGCCTGCAGGTTCCTGTCTTGAGTTCCTGCCCTGACTCCATTCACAGATAGATCTGAGAGTTGTAAGATGAAGTAAACCCTTTCTCCCCAAGTTACTTTTGGTCATGGTGTTTTATCACAGCAATGGAAAAGCAACTAACACACCACCTCTCCAGCCCTGAGTCATTTGTACACGTTTATACATATCCTCGTGTGTCTTTGTACATGTTTATACAGATGCTCACATGTCTTTGTGATATACTTTTATATGCCAGGAAATTCCGAAATTGGTTAAGTATTGAGACCTTTTCTTCTGGTCACAGTGTTAACTTTTCAGTTGTTACTCAACTTCCTTTCAGGGCATTATTGAACCTCCTGTTAGGTAAACTTAAAATTCAGTTGTGGATAATTTTGGATCCCTACGGTTGTTAGGTGTTTATTTTCCTTTAGTCAGAAAATTAAAAAAAAGAACGAAAGAGAAGAAAAAAAAATTAGTCCTGAAACACAACCACTTCTTGCCTTTCAG
Seq C2 exon
TGAGAGACTCATCGCTGCATTTGAAAGAGGGAATGAAAGGGCAGTTGACTGAGGCGTCTTCAGCCACGTCCAAAGCATACTGTGTGTACAGAAGGGAAATGGACCCAGACATTGACACAATGTGCCCGGGACAGGAAGCAGGAAGTGCGGAGGAAAAGTCTGCAGAGGAAGTTACCATGAGCCCAGCCATCACTATCATGCGGCCCATCCTCAGGTTCCTGCAGTTACTGTGTGAGAATCACAACCGGGAGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001804:ENSRNOT00000040645:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.258 A=NA C2=0.291
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF084546=RIH_assoc=PU(24.4=33.7)
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:
TCAGATCCACGGTGACTGTCA
R:
CTGAAGCTCCCGGTTGTGATT
Band lengths:
350-1704
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]