BtaINT0041992 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047998 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr11:106879329-106879833:-
Coord C1 exon
chr11:106879723-106879833
Coord A exon
chr11:106879383-106879722
Coord C2 exon
chr11:106879329-106879382
Length
340 bp
Sequences
Splice sites
5' ss Seq
CCCCACCCC
5' ss Score
-31.46
3' ss Seq
CTTCTCTCGCTCCATTTCAGGGC
3' ss Score
10.77
Exon sequences
Seq C1 exon
CCTCCGCCCCGCCCCTCCGCCCCGCCCCTCCGCCCCGCCCCTCCGCCCCGCCCCTCCGCCCCACCCCCTCCGCCCCGCCCCTCCGCCCCGCCCCGCCCCTCCGCCCCGCCC
Seq A exon
CACCCCTCCGCCCCGCCCCACCCCTCCGCGGTCTGCCTCGCTTTGCCTCAGGAGGGTCTGCAGAGCATCGAGTCCTACAGTTCAGGGTTCAGGATCAGGGTCAGCCACGGCCCCAGGAGCAGACACCTGGGCAGGAGGCTGCCCTCTGAGGCCTCTGGAAGGCGAGCGGCGGCCCCGTCTGGCCCACCGCACAGGGAATGATGCTCTGGGGGGAGCCCCCTGCTCTGGGGAGCCCTGAGGTGCCAGGCTGGCGGGAGGCATGGGCCGGCTGTGTGGACGCAGCCCTGTGAGTCCAGCGCGCTCTGGGAGGGTGGCTGACGCTTCTCTCGCTCCATTTCAG
Seq C2 exon
GGCCCCGTCGGTTTTCCCGGAGATCCCGGTCCCCCCGGAGAACCCGGCCCCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047998:ENSBTAT00000063052:57
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(6.2=10.8),PF0139113=Collagen=PU(11.1=18.9)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=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:
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