RnoINT0039787 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83391665-83392066:-
Coord C1 exon
chr16:83391920-83392066
Coord A exon
chr16:83391782-83391919
Coord C2 exon
chr16:83391665-83391781
Length
138 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GATTATCTGACATCTTACAGGTT
3' ss Score
8.35
Exon sequences
Seq C1 exon
GTGCTCCTGGCTCTATGGGATCCCCAGGCATCCCGGGCATCCCCCAGAAGATTGCTGTCCAGCCTGGGACCATGGGTCCCCAGGGCAGGAGAGGCCTTCCCGGTGCACTGGGAGAGATGGGGCCTCAGGGCCCTCCTGGAGATCCAG
Seq A exon
GTAGGGCTCTGGCTTTGGACCCTGTCCTCTCCTGGGAAAAGGCCTCCAGTCCCTTCTTCTCTGCACCCACCTCTGTCCTCTTCAGCAGGACACCACACTGCTAAGAAAAGTAACACCCGATTATCTGACATCTTACAG
Seq C2 exon
GTTTCCGAGGGGCCCCCGGCAAGGCCGGTCCCCAGGGCAGAGGTGGTGTGTCTGCTGTTCCAGGGTTCCGGGGAGACCAAGGGCCCATGGGACACCAGGGTCCGATTGGCCAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(27.0=34.0),PF0139113=Collagen=PU(57.4=62.0)
A:
NA
C2:
PF0139113=Collagen=PD(40.7=55.0),PF0139113=Collagen=PU(61.0=90.0)
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:
TGCTCCTGGCTCTATGGGATC
R:
AATCGGACCCTGGTGTCCC
Band lengths:
253-391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]