BtaINT0041249 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37091510-37091840:+
Coord C1 exon
chr19:37091510-37091578
Coord A exon
chr19:37091579-37091795
Coord C2 exon
chr19:37091796-37091840
Length
217 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TTTTTCTTTTCCTTCCATAGGGT
3' ss Score
13.39
Exon sequences
Seq C1 exon
AACTTTGCTCCCCAGTTGTCTTACGGCTATGATGAGAAATCAACAGGAATTTCCGTGCCTGGTCCCATG
Seq A exon
GTGAGTCATCAGCAGACAACATAGAGGACAGAAAAAGAGCAGACGGGCCAGTGAAGGCACATAGGGTGGCATAGATAACTTGGGAGGTCAAGATGACCTTTGGGACTTCAGAATCCAGACAGAACATGAGGCAGCTGGGTGGGCCGAACAGGAACCATGGGAGATAAACTTTACTACCGAGGCTTCACTATGGCCTCTTTTTCTTTTCCTTCCATAG
Seq C2 exon
GGTCCTTCTGGTCCTCGTGGTCTCCCTGGCCCCCCTGGCGCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:6
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=PD(8.8=21.7),PF0139113=Collagen=PU(6.5=17.4)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development