RnoINT0083974 @ rn6
Intron Retention
Gene
ENSRNOG00000000599 | Lama4
Description
laminin subunit alpha 4 [Source:RGD Symbol;Acc:1560062]
Coordinates
chr20:44175975-44177599:+
Coord C1 exon
chr20:44175975-44176117
Coord A exon
chr20:44176118-44177460
Coord C2 exon
chr20:44177461-44177599
Length
1343 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
AGGACTGTTTCCTTTTCCAGGAC
3' ss Score
10.16
Exon sequences
Seq C1 exon
ATCTCAATCATTTACCACAATGACAAGAAAATGATTTTGGTGGTGGACAGACGGCATGTTAAGAGCACAGACAATGAGAAGAAGAAGATACCATTCACAGACATCTACATTGGAGGTGCGCCCCAAGAAGTCTTACAGTCCAG
Seq A exon
GTAAAGCCTTGTGAATATATAGCTTTTCACTGCTAATGATAAGATAAAACTAAAATTTAAAAAATTAGAATAGGGACAAAAGCAACCAAACATCAAAAAGAGCCAAAGAAAAGGCAGGAGAAACATATAGATGCAGACAATATGTTGGCGCATAAAACGGGAAACCATGATTTGTATACACAAAGGATCTGTAAGGTTTTTAAAAAACAAAACAACAGTGCTCTGACGACATTATGAGACAAAGATGTTGTTGTGTTGGTCACTTACTGCTGAGAATGGGACCTACCCTAAAGAGTGGTTTGTCTGGGCTGGGTGGTGGTAGCACACAGCCTTAGTCCCAGTACTCGGCAGACAGAGGCAGAGGCAGGCTGATCTCTAAGTTTGGGACCATTCTGGTCTACAGAGAGAGTTCCAGGACAGCCAGGGCTATAAAGAGGACCTGATCTCAAGACAGCACCGAGGGGAGGAGAAGGGATGGATGGGGGGAGAGGAGAGAGGAGAGGGAGGGAGGGAGGGAGGGAGGGACAGACACAGACACAGAGAGACAGAGAGACAGAGAGACAGAGAGAGACAGAGAGAGCTTTGTTTCTTCAGTAAGAATCCCTTGAAGAAAACTAATTTTTCATTTGCAGGTAGCTGTCAATTGAAGAAGCTTCTGGGTTAGGGATAGGGATGTCTGTCCACTTCTCCCTTCAGCTCTAGGACCCCATCTGGTGCAGACCTGCACAGGCCCTGAGGTCCAGCCATCTGACATTCTCTAGGGCTTGCCTCTAGCTTTCCTTGATTAGAATATGCTACAAATAAGGCCAACCCCATCAGAAGATCTCTGAAAGCCTGAGGTCAAATCCTATCTTGGAATTTATTATGTAAGAAAACAAGTTTCTTTCCAATTTCTATGAAATTGCCAAGAGTATTTTCTATCTGTTGCATATCAACTCGGTCTCAAGAATTTATTTAAAAAATTGAATGCTGACATTCATAAATATATAATAATATATATATCATTTGATCATTAAAGAAGTAGCAATTGAAAATGGAAGTTAAAAGGTTTTGAAAACTATAAAGTAAGTGAGTTGTTCTGACTTGAAGAAGTTTACTGGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTGCCTAGCAAACGCAAGGCCCTGGGTTCAGTCCCCAGCTCCGAAAAAAAAAAAGAAAAAGAAAAAGAAAAAATGAAGAAGTTTACTACACATAAAGGTTTGCACTTGTCAAAAAAGCATGAGGATCTAAATGGTTTTAAAGCTACTGAGACTGTGAGTCAGGAGATACCATATATATATATATTTACCTATGAGGACTGTTTCCTTTTCCAG
Seq C2 exon
GACCCTAAGAGCACATCTTCCCCTAGACATCAACTTTAGGGGATGCATGAAGGGTTTCCAGTTCCAAAAGAAAGATTTCAATTTACTGGAGCAGAAAGAAACCTTAGGAGTTGGTTATGGATGCCCAGAGGACTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000599:ENSRNOT00000000737:25
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=0.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=FE(35.6=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(18.2=51.1)
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:
TCTCAATCATTTACCACAATGACAA
R:
GGAGTCCTCTGGGCATCCATA
Band lengths:
278-1621
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]