BtaINT0040838 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14939321-14939671:-
Coord C1 exon
chr9:14939522-14939671
Coord A exon
chr9:14939441-14939521
Coord C2 exon
chr9:14939321-14939440
Length
81 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
TGCCAGTGGTGTCCTTTCAGCCC
3' ss Score
6.14
Exon sequences
Seq C1 exon
GGATGGAGTGTCTCACCCGGGCTGAAGCAGACATCGTGCTGCTGGTGGATGGATCGTGGAGCATCGGCCGGGCGAACTTTAGAACCGTCAGGAGCTTCATTTCTCGTATTGTGGAAGTCTTTGAGATTGGCCCCAAAAGAGTACAGATTG
Seq A exon
GTAGGTCTCACAACATTGACGGCATTCAGATGTCTTCATCAGGTTCGCTTACATATGCTAATGCCAGTGGTGTCCTTTCAG
Seq C2 exon
CCCTCGCGCAGTATAGTGGGGACCCCAGAACAGAGTGGCAGCTAAATGCTCACAAAGACAAGAAGAGCTTGCTGCAGGCCGTGGCGAACCTGCCTTACAAAGGAGGCAACACCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.049
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=78.4)
A:
NA
C2:
PF0009223=VWA=FE(23.1=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:
GGGCGAACTTTAGAACCGTCA
R:
CTTTGTAAGGCAGGTTCGCCA
Band lengths:
183-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]