RnoINT0087332 @ rn6
Intron Retention
Gene
ENSRNOG00000022312 | Lrsam1
Description
leucine rich repeat and sterile alpha motif containing 1 [Source:RGD Symbol;Acc:1564403]
Coordinates
chr3:11972813-11974406:-
Coord C1 exon
chr3:11974261-11974406
Coord A exon
chr3:11972939-11974260
Coord C2 exon
chr3:11972813-11972938
Length
1322 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CATGGTTGCTCTCTCCGCAGGCC
3' ss Score
11.46
Exon sequences
Seq C1 exon
AGTTGAAACCACCCAAGAATGAGGTCTTTGGTGTCTCTGAGCCCCCCACAGCCCCTCAGGAGCTTCCTGAGTCCGTGAGACCATCTGCCCCGCCAGCTGAACTGGACGTGCCGACCTCAGAGTGTGTTGTGTGCCTGGAACGTGAG
Seq A exon
GTAAGTGTGGGGAGACGCTACAGATCCCAAAACATGGGACACCAAAATGACCCGAGTCCCATGACCCGATATGCGCAATGCTAACATTGTCTAGAATCTATTTTCCCCCAGAGGAAGGATTTTCCCTCAGCTTATTAACTATATTAGGGAAGATTTCCCCATCATGACTCAGCAAGAAGATGGTTCTCCTAACCAGGCCTTTCTAAGATTGTTGCAAAATTAACACTTATTGCAAAAAGTCAACATTCCAGTGCTTAAAGCACAGATCCTCCTTCACCTCCACTGAGGGATCAGACCTCAGTGTAGCCAGGGCTGGCACAGTGGCACAGGCCTGCAATCGTAGTTCATGAGACGTGAAAAGGGCAGGAGCCCTGTGAGTCTGAGGGCTGTGTAGCAAGACCCTGTCTCCCTGGCTGGGGGGATGGCTCGTGTCTGCTGCTTTTCCAGGAACCCAGGTCGGTTCCCTGCACCCAAGTCAGGTGGCTCACAATCTAAGGGGGTCGACACCCTCTCTACACTTCTTGAATAGAACATGCACATTGGTAAATAAGGCTGCCTGACTCCATGGCTCTCTGACCTTCAGAAGCCTGGGGTGCTGGAGGGCACAGTGGTTAGAACTCTAACCAAGTTCCTATCCTCAGGCTTTGAAAGGGACTCCCAATTTCTCTCTCTCTCTCTCTCTTTTTTTTTTTTTTGTAATCTATTTTTATATTTTATTTATTTAATGTATGAGTGCTCTGCTGCATATGCATCCACCTGCCTGAAGAGGGCATCAGATTCCCCTATAAATGGTTGTGAGCCACCATGTGGTTGCCTGGAATTGAACTCAGGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCCATTTCTTGATATGATAGATGACTTTGAAGCAGTTGGAGACGTCTCAGGACATTATATATACTGAGGGGTTGTGCTAAGGCAGAGTCAGGGAACACACACAAGGCTAGTGACCTGTAAGGCTGAAGTCATTTTAGGCCAGGCATCAGACTTGGGCAAGTGTGAACACAAAATAGTTACAAATCAGTGGAGAGCCAGGAGCGGTACACACCTGGCATCCCAGAACCGGGAGTAGAGGCAGCTCTTGGCCTAGTAGCAGGCACTTGGCCTAGCAGGGACTGAGGAAAGAGCATTTGGATTGTAGATGTTTGACTGCTGTTGTGATCCGTAGAGAAACAGGTACAAAACTGCCAACAGGCCTGACTGGGTTTTCACACCCGCTGGGGCTGTGATGTGGTCATGGCCCCAAAGCTGAGCAGCCATGGTTGCTCTCTCCGCAG
Seq C2 exon
GCCCAGATGGTCTTCCTCACCTGCGGCCATGTCTGCTGCTGCCAGCAGTGCTGCCAGCCGCTGCGCACCTGCCCACTGTGCCGCCAGGAGATCTCCCAGCGCCTCCGGATCTACCACAGCAGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022312:ENSRNOT00000060186:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139201=zf-C3HC4_3=PU(23.9=22.4)
A:
NA
C2:
PF139201=zf-C3HC4_3=PD(71.7=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGAAACCACCCAAGAATGAGGT
R:
TCAGCTGCTGTGGTAGATCCG
Band lengths:
270-1592
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]