GgaEX1025985 @ galGal4
Exon Skipping
Gene
ENSGALG00000012536 | GALNT13
Description
polypeptide N-acetylgalactosaminyltransferase 13 [Source:HGNC Symbol;Acc:HGNC:23242]
Coordinates
chr7:35218398-35224558:+
Coord C1 exon
chr7:35218398-35218532
Coord A exon
chr7:35222347-35222545
Coord C2 exon
chr7:35224418-35224558
Length
199 bp
Sequences
Splice sites
3' ss Seq
ACCACTTTTCTGTCATGCAGACC
3' ss Score
9.32
5' ss Seq
GAGGTTGGT
5' ss Score
6.36
Exon sequences
Seq C1 exon
GTGTTTTCCTACACGGCAGACAAGGAGATCCGCACGGATGATCTGTGCCTGGACGTGTCGCGGCTGAACGGCCCGGTGACCATGCTCAAGTGCCACCACATGCGGGGAAACCAGCTCTGGGAGTACGATGCTGAG
Seq A exon
ACCCACACATTTCTACACATAATCACCCAGTCGTGCCTGACACTCAGCAGGATAGAGGATGGCACCCATGGTCCCACCGTGGAGGCTTGCAATGGTAGCCCCTTGCAAACGTGGATGCTAAGGAACTACACCAGGCTGGAAGTCTTTAGAAACGTTTTTTACAGCCCCACTGATTATTTCCTTTAACAAGCTGTTGGAG
Seq C2 exon
AAGCTCACCCTGAGGCACGTCAACAGCAACCAGTGCCTGGACGGGCCGTCGGAGGAGGACAAGCTGGTCCCCAGCATGAAGGAGTGTGCGGGCGGCCGGTCCCAGCAGTGGCTGCTGCGCAACATGACGCTGGGGGCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012536_CASSETTE4
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=0.174
Domain overlap (PFAM):
C1:
PF0065217=Ricin_B_lectin=FE(37.0=100)
A:
PF0065217=Ricin_B_lectin=PD(30.8=59.7)
C2:
PF0065217=Ricin_B_lectin=PD(30.3=76.6)
Main Inclusion Isoform:
ENSGALT00000020475fB7783
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGACAAGGAGATCCGCAC
R:
CCCCCAGCGTCATGTTGC
Band lengths:
256-455
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]