BtaINT0041981 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106891792-106892026:-
Coord C1 exon
chr11:106891937-106892026
Coord A exon
chr11:106891846-106891936
Coord C2 exon
chr11:106891792-106891845
Length
91 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CACACCCCGTTGCTTTGCAGGGG
3' ss Score
8.54
Exon sequences
Seq C1 exon
GGTGACCCAGGCCCCGCCGGCCTTCCTGGGAAAGACGGTCCCCCCGGGCTGCGAGGCTTCCCTGGAGACCGAGGCCTTCCTGGTCCAGTG
Seq A exon
GTGAGTGAGGGGTCCGCCGGGGGACGGGTTGGATGTCCCTCCTGGGGAGGCTTCTCCCTGCGGCCCCCTCTCACACCCCGTTGCTTTGCAG
Seq C2 exon
GGGGCGCTTGGACTGAAAGGCAGTGAAGGCCCCCCCGGCCCACCAGGCCCCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:47
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(21.4=50.0),PF0139113=Collagen=FE(40.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.6=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:
CCGGCCTTCCTGGGAAAGA
R:
GGCCTTCACTGCCTTTCAG
Band lengths:
105-196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development