BtaINT0041251 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013103 | COL1A1
Description
Bos taurus collagen, type I, alpha 1 (COL1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001034039]
Coordinates
chr19:37091991-37092279:+
Coord C1 exon
chr19:37091991-37092044
Coord A exon
chr19:37092045-37092225
Coord C2 exon
chr19:37092226-37092279
Length
181 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TCTCTTCCTGTCACCTCTAGGGT
3' ss Score
11.78
Exon sequences
Seq C1 exon
GGTCCCCAAGGTTTCCAAGGCCCCCCTGGTGAGCCTGGCGAGCCAGGAGCCTCA
Seq A exon
GTAAGTGGCCCCTGATTTGCATTCTCTATGCAAATATACACCCTCTCTACAAATATATGGATTCTCCTATTGAAGGACCACCATCTGGAGTCTTTGTTACTTCCTTCTTCCAATCCTAGCCTTCCCCTTCTTTTCTCCTTATCCTGGTCATTCTAACATCCTCTCTTCCTGTCACCTCTAG
Seq C2 exon
GGTCCCATGGGTCCCCGTGGTCCCCCTGGCCCCCCTGGCAAGAACGGAGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013103:ENSBTAT00000017420:8
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(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.4=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:
GTCCCCAAGGTTTCCAAGGC
R:
ATCATCTCCGTTCTTGCCAGG
Band lengths:
107-288
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development