BtaINT0041221 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37096756-37097053:+
Coord C1 exon
chr19:37096756-37096809
Coord A exon
chr19:37096810-37096999
Coord C2 exon
chr19:37097000-37097053
Length
190 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
CTTTTTTACTCTTTCCCCAGGGT
3' ss Score
10.73
Exon sequences
Seq C1 exon
GGAGAGCCTGGAAAAGCTGGAGAGCGAGGTGTTCCTGGACCCCCTGGCGCTGTT
Seq A exon
GTAAGTATCTCCTTTTGTTCCCCGTCCCTTTCCCGCCCATGTCCCATCCCTATATCCTGCAGAAGGGATATGAGGCTCCAGCCCATCCCTAGGGCATCAGGACCCCCAGCTCCAGGCCCCTTACCTGTGCTGTCTTCCTCAGCTGCCCACCCACCTCACCACTCTAACCCCTTTTTTACTCTTTCCCCAG
Seq C2 exon
GGTCCTGCTGGCAAAGACGGAGAAGCTGGAGCTCAGGGACCCCCAGGACCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:26
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=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:
GGAGAGCCTGGAAAAGCTGGA
R:
CAGGTCCTGGGGGTCCCT
Band lengths:
106-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development