BtaINT0041302 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013472 | COL1A2
Description
Bos taurus collagen, type I, alpha 2 (COL1A2), mRNA. [Source:RefSeq mRNA;Acc:NM_174520]
Coordinates
chr4:11634236-11634434:+
Coord C1 exon
chr4:11634236-11634289
Coord A exon
chr4:11634290-11634380
Coord C2 exon
chr4:11634381-11634434
Length
91 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
GGGGTCTTCTGTTTTCCCAGGGT
3' ss Score
7.05
Exon sequences
Seq C1 exon
GGCCCTCAAGGTTTCCAGGGACCTCCGGGTGAGCCTGGTGAACCTGGTCAGACT
Seq A exon
GTGAGTACTTTTCCCCCTGTGTGATAAGTATTTTTTTCAAGAGGTTTATTAATATAACATTAACAAAATGAGGGGTCTTCTGTTTTCCCAG
Seq C2 exon
GGTCCTGCTGGTGCTCGTGGCCCGCCTGGCCCTCCTGGCAAGGCTGGTGAGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013472:ENSBTAT00000033863:8
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(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100),PF0139113=Collagen=PU(17.7=77.8)
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:
TCAAGGTTTCCAGGGACCTCC
R:
ATCCTCACCAGCCTTGCCAG
Band lengths:
103-194
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]