BtaINT0040753 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40529561-40529991:+
Coord C1 exon
chr3:40529561-40529713
Coord A exon
chr3:40529714-40529901
Coord C2 exon
chr3:40529902-40529991
Length
188 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCA
5' ss Score
6.28
3' ss Seq
TCTTTTGAATTCACTATTAGGCA
3' ss Score
5.44
Exon sequences
Seq C1 exon
AAAAAGAAATTCAGTTTCAAAATGAAGATGAAGACAGTGGCCACTAATTCAAAGAAAAAGTCCAAAAAGTTTACACCCCCTAAATCTGAAAAATTTGCATCCAAGAAGAAGAAAACTTATCAAGCAGCAGCAATGGCCAAGCTAGGGGTAAAG
Seq A exon
GTAGCAAAGAAAAAGCAATCAAGATCTCTCCTAGATAAGCTGGAAGATCTCTGATGATGAGTCATTCCTAACCCAACTAGATAAATACTCATTTGGCTAATACAATATCCTAATTAATTATGCTTTCCATAGATTTTGGATTACCTTAACATTTTTACTAATTACTTTTCTTTTGAATTCACTATTAG
Seq C2 exon
GCAAATATTGTTGATGATTTTCAAGAATACAACTATGGGACAGAAAGTTACCAGACGGAAGCTCCTAGGAGTGTATCTGGATCAAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.255 A=NA C2=0.633
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAATGAAGATGAAGACAGTGGCC
R:
CTCATTTGATCCAGATACACTCCT
Band lengths:
226-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]