BtaINT0040733 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40601555-40601960:+
Coord C1 exon
chr3:40601555-40601644
Coord A exon
chr3:40601645-40601906
Coord C2 exon
chr3:40601907-40601960
Length
262 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAA
5' ss Score
7.46
3' ss Seq
TTGCTTTTCACTTTTCCCAGGGT
3' ss Score
8.27
Exon sequences
Seq C1 exon
GGTGACCCAGGTCCTCAAGGTGTCTCAGGGAAAGATGGACCAGCAGGACTACGTGGTTTCCCAGGTGAAAGAGGGCTTCCTGGAGCTCAG
Seq A exon
GTATAATTAACATATTAATGAAACATGTAAATAAGATTGCTTTTTAGAAGCATTCTTTTGGTCTCAACTAAATAAAGATTCATGAGTAATTAAAGGGAAATACGTGAACATATGCACTGGTTGTGGTAAAACATAGAGCAATAGATTAATGTATTTGTGTCTGGAATCACTTCCTGACATTCTCATTATTTCAGTCATACATCACCTCTTATTTATATTCAATTCATATCAATTCATTTTCTTTGCTTTTCACTTTTCCCAG
Seq C2 exon
GGTGCCCCTGGATTGAAAGGAGGAGAAGGTCCCCAGGGCCCACCAGGTCCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:41
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(34.9=100),PF0139113=Collagen=PU(24.7=70.0)
A:
NA
C2:
PF0139113=Collagen=PD(12.0=55.6),PF0139113=Collagen=FE(20.0=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]