BtaINT0040756 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40667706-40667889:+
Coord C1 exon
chr3:40667706-40667741
Coord A exon
chr3:40667742-40667835
Coord C2 exon
chr3:40667836-40667889
Length
94 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
TTGCTTATTCTTTCTAATAGGGA
3' ss Score
8.52
Exon sequences
Seq C1 exon
GGTCCTCAAGGTCCAAAGGGCACTAAAGGCTCTACG
Seq A exon
GTAAGTACCTTTCCCTTTAGCATTTAAAGTTTTCAGTGATGCCTACTCAAATGTTTTGGTCTCCATTTATTTTGTTGCTTATTCTTTCTAATAG
Seq C2 exon
GGACCTGCTGGCCAGAAGGGTGACAGTGGTCTTCCAGGGCCTCCTGGGCCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:62
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(12.1=100),PF0139113=Collagen=FE(18.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.9=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:
GGTCCTCAAGGTCCAAAGGGC
R:
GAGGCCCTGGAAGACCACT
Band lengths:
79-173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]