BtaEX0015290 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000005562 | GALNT13
Description
Bos taurus UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) (GALNT13), mRNA. [Source:RefSeq mRNA;Acc:NM_001076886]
Coordinates
chr2:41791846-41806099:-
Coord C1 exon
chr2:41805965-41806099
Coord A exon
chr2:41796136-41796332
Coord C2 exon
chr2:41791846-41791986
Length
197 bp
Sequences
Splice sites
3' ss Seq
TTATTTTCTTTGTCAAACAGACC
3' ss Score
8.69
5' ss Seq
GAGGTTTGT
5' ss Score
6.36
Exon sequences
Seq C1 exon
GTATTTTCTTATACTGCTGACAAAGAAATCCGAACCGATGACTTGTGCTTAGATGTTTCTAGACTCAATGGACCTGTAATCATGTTAAAATGCCACCATATGAGAGGAAATCAGTTATGGGAGTATGATGCTGAG
Seq A exon
ACCCACACTCTTCTTCACATAATCACCCAGTCCTGTCTCTCAGTAAGCAAAGTAGCTGATGGCTCCCAACAGCCCGCTGTGGAAATATGTAATGATAGCCCTTTGCAAAAATGGCTTCTAAGAAACTATACAAGAATGGAAATTTTTAGAAATATTTTTAAGAATTCTACTGATTACTTTCTCAAATAATTTTGGAG
Seq C2 exon
AGACTCACCTTGAGACATGTTAACAGTAATCAATGTCTAGATGAACCTTCTGAAGAAGACAAAATGGTGCCTACCATGCAGGACTGTAGTGGAACCAGATCTCAACAATGGCTGCTAAGGAACATGACTCTGGGGGCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005562_MULTIEX1-4/4=3-C2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.304
Domain overlap (PFAM):
C1:
PF0065217=Ricin_B_lectin=FE(37.0=100)
A:
PF0065217=Ricin_B_lectin=PD(30.8=58.7)
C2:
PF0065217=Ricin_B_lectin=PD(30.3=76.6)
Main Inclusion Isoform:
ENSBTAT00000057469fB2916
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCGAACCGATGACTTGTGC
R:
GCCCCCAGAGTCATGTTCCTT
Band lengths:
245-442
Functional annotations
There are 2 annotated functions for this event
PMID: 22186971
The study identifies and characterizes enzymatically active splice variants of GalNAc-T13 that differ in the sequence of their lectin domain (via inclusion/exclusion a penultimate exon that changes C-terminus (HsaEX0026914)). The variants differ in their affinities for glycopeptide substrates.
PMID: 27913570
Polypeptide GalNAc-transferase 13 (GalNAc-T13) splice variants with changes in their lectin domains were characterized by in vitro glycosylation assay: one (delta39Ex9) (alternative splice acceptor site in exon 9, not in VastDB) was inactive while the second one (Ex10b) (cassette exon, HsaEX0026914) had essentially unaltered activity.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development