BtaINT0040726 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40583571-40583784:+
Coord C1 exon
chr3:40583571-40583624
Coord A exon
chr3:40583625-40583739
Coord C2 exon
chr3:40583740-40583784
Length
115 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
TTTTGTGTTGTTTTTCCCAGGGC
3' ss Score
11.01
Exon sequences
Seq C1 exon
GGACCTCGAGGTTCAAGAGGAGCAAGAGGTCCCACTGGGAAACCAGGTCCAAAG
Seq A exon
GTACTGTCAGAACTTGTTCCATTTGGGCTTGTCTGTAGGTTCCTCTTCCAGAGGACGGCTGTTACCGGAAGGAGTCAAAACTGATTTTTTTCTGTTTTTGTGTTGTTTTTCCCAG
Seq C2 exon
GGCACTTCAGGTGGTGATGGCCCTCCTGGCCCTCCTGGTGAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.892 A=NA C2=0.750
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCGAGGTTCAAGAGGAGCA
R:
TCTTTCACCAGGAGGGCCAG
Band lengths:
96-211
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]