BtaINT0040839 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14939059-14939440:-
Coord C1 exon
chr9:14939321-14939440
Coord A exon
chr9:14939224-14939320
Coord C2 exon
chr9:14939059-14939223
Length
97 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTTTTAACAATCCCACTAGGGA
3' ss Score
6.8
Exon sequences
Seq C1 exon
CCCTCGCGCAGTATAGTGGGGACCCCAGAACAGAGTGGCAGCTAAATGCTCACAAAGACAAGAAGAGCTTGCTGCAGGCCGTGGCGAACCTGCCTTACAAAGGAGGCAACACCCTCACAG
Seq A exon
GTGAGCCAGATGGTTCAGGGCGCTGTCGGCTCTCGCTTTTGTCCGAGCTCGTGGCTGAATAATGATGTGGCTGATTCTCTTTTAACAATCCCACTAG
Seq C2 exon
GGATGGCCTTGAATTTCATTCGCCAGCAGAGCTTCAAGACCCAAGCTGGCATGAGACCTCGAGCTCGAAAAATCGGTGTTCTTATCACTGATGGAAAATCCCAGGATGATGTTGAGGCACCTTCCAAAAAACTCAAGGATGAAGGCGTGGAACTGTTTGCCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.1=100)
A:
NA
C2:
PF0009223=VWA=FE(31.8=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:
AAGAAGAGCTTGCTGCAGGC
R:
GTGCCTCAACATCATCCTGGG
Band lengths:
181-278
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]