BtaINT0040725 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40583204-40583422:+
Coord C1 exon
chr3:40583204-40583257
Coord A exon
chr3:40583258-40583386
Coord C2 exon
chr3:40583387-40583422
Length
129 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGA
5' ss Score
7.63
3' ss Seq
GTTTGTACTGTTGTTGACAGGGT
3' ss Score
6.1
Exon sequences
Seq C1 exon
GGTTCCACTGGATTTCCTGGGTTTCCAGGTGCCAATGGAGAGAAAGGTGCCCGG
Seq A exon
GTATGATATACAAGTATACTGTTCTGGACTAATATAAGTGTTCTTACATGGGAACCTATGTCTCGGACCCAGACTCGCAATTCATTGTGATATACCGTATACTGAGGCTGTTTGTACTGTTGTTGACAG
Seq C2 exon
GGTGTAGCTGGCAAACCAGGTCCTCGGGGTCAGCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.486 A=NA C2=0.880
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.0=100),PF0139113=Collagen=PU(0.1=0.0)
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:
GGTTCCACTGGATTTCCTGGG
R:
GACCCCGAGGACCTGGTTT
Band lengths:
85-214
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]