BtaINT0041229 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37098978-37099348:+
Coord C1 exon
chr19:37098978-37099085
Coord A exon
chr19:37099086-37099294
Coord C2 exon
chr19:37099295-37099348
Length
209 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTCTTGTCCCTTCCTTTCAGGGT
3' ss Score
12.62
Exon sequences
Seq C1 exon
GGGGATGCTGGTCCCAAAGGTGCTGATGGTGCTCCTGGCAAAGATGGCGTCCGTGGTCTGACTGGTCCCATCGGTCCTCCTGGCCCCGCTGGTGCCCCTGGTGACAAG
Seq A exon
GTGAGATGGCCCACTTCTCACCTTCTTCCCTAACACAGAGCTTCCCTCGTGAGCCTGGGCACGGCTCTGCTGCAGAGGCAGCTCTTGCCACTCCAACCTGGCCACCCAACGGTGGGGTGACCAGGAGAGATGAGGACTCTCCTGGGGTCATCGGGCAGGAGTATTCAGTGTGGCACCCTGATCCTGAGCCTCTTGTCCCTTCCTTTCAG
Seq C2 exon
GGTGAAGCTGGTCCTAGTGGCCCAGCCGGTCCCACTGGAGCTCGTGGTGCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:33
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:
NO
A:
NA
C2:
NO
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:
GGATGCTGGTCCCAAAGGTG
R:
GCACCACGAGCTCCAGTG
Band lengths:
156-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development