BtaINT0040710 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40550573-40550788:+
Coord C1 exon
chr3:40550573-40550626
Coord A exon
chr3:40550627-40550743
Coord C2 exon
chr3:40550744-40550788
Length
117 bp
Sequences
Splice sites
5' ss Seq
AGGGTATAT
5' ss Score
3.89
3' ss Seq
ATTCATTATGTCCATGACAGGGA
3' ss Score
5.64
Exon sequences
Seq C1 exon
GGTGAACGAGGTCCTCAAGGTCCTCCTGGTCCTCCTGGTGAAGATGGAATAAGG
Seq A exon
GTATATGAAAGTTCATTTCTTTTAAGAAATATTTAAAATTAAAACATTAAAGAAAACCATGCTGAAATGTTGCATTGTCTGATCACATCACTATCCTATTCATTATGTCCATGACAG
Seq C2 exon
GGAGAAGATGGAGAAATAGGACCAAGGGGTCTTCCAGGTGAAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:19
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=FE(21.0=100),PF0139113=Collagen=PU(21.2=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(15.9=73.3),PF0139113=Collagen=FE(16.1=100)
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:
TGAACGAGGTCCTCAAGGTCC
R:
TTCACCTGGAAGACCCCTTGG
Band lengths:
94-211
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]