BtaALTD0005727-1/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000025210 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr12:89131113-89131805:+
Coord C1 exon
chr12:89131113-89131223
Coord A exon
NA
Coord C2 exon
chr12:89131656-89131805
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
GTTCACTGTTGGGTTTTCAGATG
3' ss Score
8.05
Exon sequences
Seq C1 exon
GTGTCAGAGGTGAGCCGGGATCCCCAGGAGCTCCCGGGGAGCCAGGAGACCGCGGGGTACCAGGAGACCCCGGCCTGCCAGGCCGGCCCGGCACAACCATCGGAGACGAAG
Seq A exon
NA
Seq C2 exon
ATGAGAAGAGAGGCTTGCCAGGTGAAATGGGACCCAAAGGCTTCACAGGAGAACAGGGTTTCCCCGCGCTGTACCCTGGCCCCCCAGGGACTGATGGGCAGCCAGGGCTCCGCGGTCCCCCCGGGCTCCCAGGACCGCCCGGCCCAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000025210-16-16,17-16-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(56.9=100),PF0139113=Collagen=PU(5.4=7.9)
A:
NA
C2:
PF0139113=Collagen=PD(30.8=39.2),PF0139113=Collagen=FE(89.3=100),PF0139113=Collagen=PU(39.3=47.1)
Main Skipping 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:
GTCAGAGGTGAGCCGGGATC
R:
CTGGCTGCCCATCAGTCCC
Band lengths:
214-553
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development