RnoINT0039111 @ rn6
Intron Retention
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148264183-148264513:+
Coord C1 exon
chr5:148264183-148264263
Coord A exon
chr5:148264264-148264387
Coord C2 exon
chr5:148264388-148264513
Length
124 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TTTTCTCCCATATTGAGCAGTGT
3' ss Score
4.8
Exon sequences
Seq C1 exon
TTTGACCTTCAGCAGGCGCACATCTACTGTGACCCGGAGCTGGTGCTGGAGGAAGGCTGCTGTGAGATCTTACCGGGAGGG
Seq A exon
GTGAGTAGCTGGCTCCTAGCACACGCTGTGCTGGAGAGGGGGCAGCCTGCACAGGGATGGCAGAGGTCTGAGGATGCATCTGCCTCTGTACTGACCCCGACTGCTTTTCTCCCATATTGAGCAG
Seq C2 exon
TGTCCCCCAGAGACCTCCAAGTCACGCCGGGACACCCAGAGTAATGAGCTCATTGAGATCAATCCTCAGACCGAGGGCAAGGTCTACACCCGCTGCTTCTGCTTGGAAGAACCTCATAACAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475:ENSRNOT00000067663:7
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=0.429
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PD(3.5=14.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTCAGCAGGCGCACATCTA
R:
CTTGCTGTTATGAGGTTCTTCCA
Band lengths:
202-326
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]