Special

RnoINT0038872 @ rn6

Intron Retention

Gene
Description
collagen type XI alpha 2 chain [Source:RGD Symbol;Acc:2373]
Coordinates
chr20:3850642-3850958:+
Coord C1 exon
chr20:3850642-3850731
Coord A exon
chr20:3850732-3850904
Coord C2 exon
chr20:3850905-3850958
Length
173 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
ACCCTAAATCTGGTTCCTAGGGC
3' ss Score
7.17
Exon sequences
Seq C1 exon
GGTGACCCCGGGCCCCCCGGGGCCCCAGGGAAGGATGGCCCCGCTGGTCTGAGAGGCTTCCCAGGAGAGCGAGGCCTCCCGGGCACTGCT
Seq A exon
GTGAGTATAACCCTGAAAGCCTATGGATACAGCTCACTATCGGATCCCCTTGATATGACACCCCGCTTTCTCTCACTGAGCCTACATCTTCCCAAAGCCCACACTTCCCGTGTCTTCTGGGGGCCCATGCCTGTGAAGTCTCACTCACCCCTCACCCTAAATCTGGTTCCTAG
Seq C2 exon
GGCGGACCTGGCTTGAAGGGAAATGAAGGCCCAGCTGGCCCTCCTGGCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000463:ENSRNOT00000045533:38
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(15.9=36.7),PF0139113=Collagen=PU(3.3=10.0)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCCCCAGGGAAGGATG
R:
GCTGGGCCTTCATTTCCCTTC
Band lengths:
106-279
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]