BtaINT0042450 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55028495-55028957:-
Coord C1 exon
chr13:55028898-55028957
Coord A exon
chr13:55028549-55028897
Coord C2 exon
chr13:55028495-55028548
Length
349 bp
Sequences
Splice sites
5' ss Seq
GAGGCCTGA
5' ss Score
-5.07
3' ss Seq
GGTTCCTCCGTGTCTCCTAGGGC
3' ss Score
8.38
Exon sequences
Seq C1 exon
GAGTGGCCGGGCAGGGGCCAGAGGACCACTGACGTCCATCAAGAGGCCCTGGGCTGTGAG
Seq A exon
GCCTGACCTTGTGCCAGGACTGCCCAGCTGAGAGATGGAGCAACAGAAAACACGACTCTCGGGTTAAGTGACACTGAGATAATCAGACATCTGCCAAAATGAACTGAAGTGACCATCTCCAAACCCATCTCATCTTCCCCCGGCTTGAGAGCATCCCCAAGACCCTAAGATAGCTCCTGCTTGATGGGCCTTTTCCCCTAAGGGTTGGGTCTGGCCCCCACAGCTGTCCCCCAGCCAATCCTGAGTCTAGGAAGTGGTGGGCAAGCCTCCTGCCCACCTCCCAGGATCCAGTGACACATCTGGGAGAGCAGTCCCCGAGGCCTGACTGTGGTTCCTCCGTGTCTCCTAG
Seq C2 exon
GGCAGGCCTGGTCCTAAAGGCATCCCCGGCATGTCTGGGCCCAGTGGAGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:16
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(14.8=45.0),PF0139113=Collagen=PU(11.1=35.0)
A:
NA
C2:
PF0139113=Collagen=FE(27.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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