BtaINT0040849 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14925511-14925992:-
Coord C1 exon
chr9:14925853-14925992
Coord A exon
chr9:14925644-14925852
Coord C2 exon
chr9:14925511-14925643
Length
209 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTG
5' ss Score
4.58
3' ss Seq
TTTTTTCCTCTTTCCTTAAGACC
3' ss Score
7.11
Exon sequences
Seq C1 exon
ACACCGTGCCAGCCCCAACAAACCTACAGATTACTGAAGTAACACCAGAGAGTTTCAGAGGGACTTGGGACCATGGAGCTTCTGATGTGTCTCTCTATAGAATCACCTGGGCGCCTTCAGGAAGCGCAGATAAGATGGAG
Seq A exon
GTAGTGTTAATTCTTTTTTTTTTTTTTTAAATATATGACCTTTGTTGCCTGAAAAGCATCGTTTCCTACTAGTGACATTTGAGCTCATGGCATGCCTCAAAGCAGGAAGAACATCTGGCTAAATGATGTCAACCAGCTGCCGTGGAGCTGTGATGCACACGGTGACTTAATCTTGTGTGGGCTTGTTTTTTTTTTCCTCTTTCCTTAAG
Seq C2 exon
ACCATCCTAAATGGAGATGAGAATACTCTGGTGTTTCAAAACCTGAACCCCAACACTCTCTATGAAGTTTCTGTTACCGCCATTTATCCTGATGAGTCAGAAAGCGATGACCTGATTGGCAGTGAGCGTACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.553 A=NA C2=0.556
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.4=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.0=75.6)
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:
GTGCCAGCCCCAACAAACC
R:
GTGTACGCTCACTGCCAATCA
Band lengths:
268-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]