BtaALTA0007746-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000021310 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:116056723-116057616:-
Coord C1 exon
chr2:116057563-116057616
Coord A exon
chr2:116056793-116056855
Coord C2 exon
chr2:116056723-116056792
Length
63 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CCCTTCTAATATTTACTTAGTGC
3' ss Score
5.49
Exon sequences
Seq C1 exon
GGGGAACCAGGACTGTTTGGAGATCCTGGGTCATTTGGATTTCTTGGCCCAAAG
Seq A exon
TGCCAGGAAACAGGAGAAGAATATTAATATTTCTAAGAAAAGTGAATGAATGAATGATTTCAG
Seq C2 exon
GGAGATCCTGGAGACCGAGGGCACCCAGGACCACCAGGGGTTTTGGTAACTCCATCTCTTCCACTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021310-20-23,20-22-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(26.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(24.6=66.7),PF0139113=Collagen=PU(4.6=12.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAGGACTGTTTGGAGATCCT
R:
TGAGTGGAAGAGATGGAGTTACC
Band lengths:
116-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development