BtaINT0041212 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37094509-37094748:+
Coord C1 exon
chr19:37094509-37094553
Coord A exon
chr19:37094554-37094649
Coord C2 exon
chr19:37094650-37094748
Length
96 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
ATTTGTTTGGCCTCCCTCAGGGC
3' ss Score
8.31
Exon sequences
Seq C1 exon
GGCAACCCTGGTGCTGATGGACAGCCTGGTGCTAAAGGAGCCAAT
Seq A exon
GTAAGTATCCTGCAGGTCTCAGAGCCGCCCCCGGTACCCGCCTTCCACCTGCCTTTGCCCTCCAGTCCTGGGCTCAATTTGTTTGGCCTCCCTCAG
Seq C2 exon
GGCGCTCCTGGTATTGCTGGTGCTCCTGGCTTCCCTGGTGCCCGAGGCCCCTCTGGACCCCAGGGCCCCAGCGGCCCCCCTGGCCCCAAGGGTAACAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(23.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(23.3=42.4),PF0139113=Collagen=PU(42.7=97.0)
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:
GGCAACCCTGGTGCTGATG
R:
GGCACCAGGGAAGCCAGG
Band lengths:
87-183
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development