RnoEX0037600 @ rn6
Exon Skipping
Gene
ENSRNOG00000005335 | Galnt13
Description
polypeptide N-acetylgalactosaminyltransferase 13 [Source:RGD Symbol;Acc:735044]
Coordinates
chr3:40610793-40624530:+
Coord C1 exon
chr3:40610793-40610927
Coord A exon
chr3:40619315-40619512
Coord C2 exon
chr3:40623975-40624530
Length
198 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
GTGTTTTCTTACACTGCTGACAAAGAAATCCGAACTGATGACTTGTGCCTGGATGTATCCAGACTCAGTGGGCCTGTAATCATGTTAAAATGCCACCACATGAGAGGGAATCAGCTGTGGGAGTATGATGCTGAG
Seq A exon
ACCCATACTCTTGTTCACATAATCACACAGTCCTGCCTCTCAATGGGCAAAGTAGCGGACGGCTCTCAACATCTTACCATGGAGACTTGTAATGATAGCACTTTGCAAAAATGGCTACTAAGAAACTATACAAGAGCAGAAGTTTTTAGAAATGTTTTTGGAAATCTTACTGATTATTTTCCTTAATGACTTGTAGAG
Seq C2 exon
AGACTCACTTTGAGACATGCTAACAGTAACCAATGTCTTGATGAACCTTCTGAAGAAGACAAAATGGTGCCTACCATGCAAGACTGCAGTGGCAGCAGATCTCAACAATGGCTGCTGAGGAACATGACCTTGGGGACATGAAGATCTTTTTTCCCAAGATGTGAAAGTCTCTACTCATTTGTTTGTCCATTATTTCAGTTTGGTGAAAATCTTAACTTTGCTGAATTAAACGTTTTAAAAATACTTTTAGTAATATAAAACACAGTTGTTTATAATTCATTTTTAGGAATGTTTATTTCCCTACTAAAAATTTGTATCTGATTGAAGAAGCACATAAAATATAAATAATAAGAAACTGTTATTAAACATTTCAATTGTTTGGGAAAAAAAACACCTTGTATTTACTTTTAAAATGTCTTCATTAGCCTCTTGTCACAAGGTTACTTGGTATTGATTTATTTGGTGTTCTAATAACAATTAAAAGAGAGATCATGTAATGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005335_MULTIEX1-2/2=C1-C2
Average complexity
C1
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=0.370
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:
ENSRNOT00000048804fB5836
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGAACTGATGACTTGTGCCT
R:
TGTCCCCAAGGTCATGTTCCT
Band lengths:
244-442
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]