GgaINT0124655 @ galGal4
Intron Retention
Gene
ENSGALG00000003340 | GBGT1
Description
globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 [Source:RefSeq peptide;Acc:NP_001025854]
Coordinates
chr17:6830389-6833835:-
Coord C1 exon
chr17:6833701-6833835
Coord A exon
chr17:6833145-6833700
Coord C2 exon
chr17:6830389-6833144
Length
556 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GTTTATGTTTGTCTGTACAGATA
3' ss Score
8.46
Exon sequences
Seq C1 exon
GCGTCAGGATGTGCTAACAGTCACACCATGGTTGGCCCCCATCGTTTGGGAAGGCACCTTCAGCCCTGAGATCCTGGACAGTGCCTACATGCCACTGAATCTCACCATAGGGGTGACAGCCTTTGCCGTTGGAAA
Seq A exon
GTAAGTGAACCATTTGGGGAGGGCCCAGTTCTCGGCTGCTTGTAGAAAGGTGCTTTGGGCTCTTCTTGTCCTCAGCAGAGCTGAAGTCTGTTCCAATCTGCAGCAAGTTTTTTTATGCCTATGTAGAACACCTCCATAGAATGGCTTGAGTTGGAAGGGACCTCAAGGGTCATGAAGCTCCAACCCCCTTGCCACAGGCAGGGCTGCCAACCTCCACGTTTAATACTAGACCAGGCTGCCCAGGGCCCTATCCAACCTAGCTTTGAACCTTGAACCCATCCAACCTGGCCTATGTGCTGTGTCCATAATCATACGAGCCTGTAAAATAACCTCGGCATCCAAGATGTCTGCAGAAATTAGAGATGTAAATGGGTCGGCCAAAGTGGGGACGATCAACTTGTTCCTTGTTCTCCACCACTCTTCACTGTATATATAACATATGCATCCTTGTAGCTGTACCCAGTAACGCTCCCTTGTCTTCATTCACTGAAGTACCCTCCGTGATCCACTATGCAGCCCCATGTCTCTGCTGTGCTGTTTATGTTTGTCTGTACAG
Seq C2 exon
ATACACGAGGTTTGTGAGCCGCTTCCTGAAGTCAGCAGAGATGCACTTCATGAAAGGCTATCGAGTGAACTACTACATCTTCACTGACAACCCCGAGATGATCCCCGATGTCCAGCTGCAGCCTGGACGAAGGTTTGATGTTGTGCACATCAAGAAATACTCCAGCTGGCAAGAGATCTCCGTGCGCAGGATGGAGGCCATAAACCTACACATAGCAGAGAGGAGCCATCGGGAGGTGGACTACCTCTTCTGCCTGGATATTGACATGGTGTTCCACAATGCCTGGGGGGCTGAGACCCTCGGTGACATGGTGGCAGCCATACACCCTGGTTATTTCAATGTCCCTCGAAGCCAGTTCCCATATGAGAGGAGGAGCTCTTCAGCAGCCTACATCCCTGACGGAGAAGGGGACTTCTACTATGGAGGAGCTGTGTTTGGAGGGCTGGTCAAGAAGGTCTACGAGTTCACCAAGATCTGCCACATGACCATCCTGGCAGACAAAGCCAATGGGATCATGGCAGCCTGGCAGGAAGAAAGCCATCTCAACAGACACTTTCTCACCCACAAACCCTCTAAGTTGCTCTCTCCAGAATATCTATGGGATGACAGGAAGCCAAAGCCCCCGGAAATTTTCCTCATACGCTTTTCCACAGTAGATAAGAACTACCAGGAGGTAAGAAATTGACCGTCTGATCCTCACAGACAGACGTTCTCCATGTGATCCAACCTGCTGAATGTTAGCTCCCAGAGAAGATGCCCCACTGTAGGTAGTTCCTCCAAAGAGTGAGAGCCTTAAAGCATTTCAGAAGCAGCAGCCGAAGTGGAGGTGAGAATGGAAAGGTTTCTATGTTCCTAATCTTTGTCAATACAAGTGTTGCACTGAGGGTTGGAGCACACCAGAAGGTATACAAAGGGTCTGCTGTCAAGTAGAAGGCTGTCCTCATAGCAAGGCTGGAAATGCTGTTGTTTGCATGTTTTCCTGAAGCTTTGTAGAGACTTAGGCAAGATTAAAACAGGCTTTGGCATCCCTGTGGAAAAAGAAAAGATCCAGATAAAGCCCTTTCCACTTAAATACCTCAATCACCCTGCTTTTAAAAAAATTATTGTTATTATTATTAATTTTCACATCTACGGTTCAAGGACTTTGTAAGGATCAGCTTGCCCTTGGTGCAGGTTATCCCTGCTCAGTGTGCAGCAGTGATGGACCTCTTCTCAGCAGTGAGATGCAGGAATCCCTGACAGACCAGCAGTGCCACTTCACATCGCACTTACCTTCCACTTCCCAGCTGTGTTTTGGGCACCCAAGTTCAGGCTGAACTGGCACAGTTCAGACCCAGAGAGCGCTGTTCCAATCACAGATGTGCTCTACAATCTCCTTGCCAGCTCACACGTCTCTGGCGCTCGTGTAATCTTTTCCATGGTGTGAGAGGTCCATGTGCTTACTCTCTGCTTCAGTTCTCTCCAAATTTTCTGAGCACTGTAAAATGGCCAGAAGCTGTTGGAGCTGACAGTGAGAGCTGGAGCATTTCCTGCAGACAGGGTGGCTTCACTCCATGAGATGCTCTCTTGAAGCCGCATGTTCAGCTGGGAGCTGGAGCTAGGCTGGGCTTAACCTTTTCTTTGCATGAATGTGGTGAGAAGCTGAGCCAGGCACTCTGCAGCTTTCCAAGCCTGCGAGCTCGTAGGGCAAACAGGTGGGGAGGGTGTCCAAACACAGGGGAACAGCTGTGCCTTGCCAGCAGCAGCTGCAAAACGGATCATCAGCTGAGGTTACGGTGTGGAGGTCTGTGTGTTGCCTCCCTGCTACAGCACAATGGCTGTGAGCATCTTCCCTGTGAGCTCCTCAGGAGTGCTGCCAGTGGGCGCTGCGGGTCTGTGCCAGCTGTGCCAGCCTCACTTGCTAGGAAGATCTTTATCCCAGTATTTCTAAGGATGTGCCAAAACCAGGATTATTACTGACCGTCTTCTAGTTCCAAAACAATTGTGTCCAAAGCCCACGCCTGACTCCGGGGTCTCATTATGTTGGTGACTACGTGTGGGCATATGGAGCCCTTTGCAAGCCAGAAGGAGCTGTCTGGTTCAATCTCCTGCATGGGGTTAGCTGGATAATTTTATCTCCTGATGTCAGTATCAGTGTCATAAATACATGGCTGAGCTGTGCTGCATCTCTCAGAAGAGAATTCAGGCCCAACACAAACATCAAGTGATACAGATGCCACAAAGCCATGGTCAGCTCCTCCTGTGCCTTAATTCTGCTCCAAGTCAGGCTCTGTTTTTGGTCATTCTGCCATGCTAGATTATCCAAAGTCCTGTGCAGATATTCATATTCATGCACCTATGTCTCTGGGGAGCTGCAGGAGGATGCTCTGCTCCCCATAGCAGTGTGGGAGATGCTCTCTCAATCAGCACGTCTCTAATTAACGAGAGCCCAGACTTCTGCCATCACCTCCTGCTGATTAATCCCCTTCCCCCAGCACCATGCTTTGCTTCTTGTGTTTGCGTTGTGCAGCCTGAGCCCCACAGGCTGGGGGGGAGTTCCACAGGGGCTGCTTTCTGGTCTTAATTTTTCACTAATGCTCACAGGAAAACTGGGGCACATAGTAGCAAAGCATGGTGTGGTGCTGCTGCATGTGGGGGCTGCCACGGGGGGACAATGCTGTGTCTCATGTCCTTATGCCAAGGGAGTTTAGACTTGGAAACACACTTGCTGTACCGCATGGAAAGTGAATCAGCACATGCAAATAAAATCATCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003340:ENSGALT00000005285:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF034148=Glyco_transf_6=FE(13.4=100)
A:
NA
C2:
PF034148=Glyco_transf_6=PD(67.4=99.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCGTTTGGGAAGGCACCTT
R:
CCAGGCAGAAGAGGTAGTCCA
Band lengths:
353-909
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]