GgaINT0008336 @ galGal4
Intron Retention
Gene
ENSGALG00000003743 | VPS37B
Description
vacuolar protein sorting 37 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:25754]
Coordinates
chr15:5234814-5237255:+
Coord C1 exon
chr15:5234814-5234896
Coord A exon
chr15:5234897-5236029
Coord C2 exon
chr15:5236030-5237255
Length
1133 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GATTATTTCATATTTGACAGAAT
3' ss Score
5.45
Exon sequences
Seq C1 exon
ACAGACAATCCAGTAATGCCTCACTGGAGACACTGCTAGCACTCCTTCAGACTGAGGGGGCTAAGATTGAGGAAGACACGGAG
Seq A exon
GTAAGGACAGTACGCTTTGGTTCTGTCCCTTTCTAACCATTAGTGGAGATTCTGGGTGTACACAGCTGAAATATACCATTAAACATGTAATAATCTAAAGGGATGTTTTCGAGAATGTGATCTGGTCTTTGCTTTGAACGTCATTAACAGTCATTTGATTTCAGTGGGATTTCTCTGAGTAATTTTTTACTCTTGAGATCTTTGAAGTTTAAGAAGCTGCTCTTTTTCAGAAATGAAAGCCAAACCCTCTTAGTTCCTTGGCATTGCCTTCAAACTAATAACGTATGAACGTGGAAATCTTTTTAATGGTGTCTGCCTGGTGTATGTATTGATCCATTACAATTGTCAATTAGTAACCTAATGAAAAACTGTGCCTGTAATGGTTTGTACGATGAGAGGACTGACTTTGCAGCAATTCTGGTGGAATATTCCATTGTGATTTCAACGTATCTGTCTAGATGCCAGTGGTCAGTGCTTGCTGGGATATGAGTGCTTAATGGGTGGTTTGTTTTTAGAGCAATGGAAGTGGTTAGTTTTGTTTGCAGATCTGCCTGTAGGACATTCTCTGTAACTACATAGCATCAGGGGAAAAGATCTTTTTGGCCCTGAGTTGTGATTACAAAAAGCTGTTCCCAGGACAAGTTGAATTTCATGATTATATGTGTTGTTACCTCTTTGAATTATTAAAGCATCGTTTACCCAAAGGTTTGCTTTGCCACAAGTAAGCATGAGTCTTAAACCTGGTTTTGCAATAATCTACCTCCCTGTGCTGAGTTCTCCATGTTTCTGTTGGCGTTGCAAGCAGTTCTAAACTGTGATTCAGCTTTGCTGGCAATCTGAAAAGCGGTTGCGCTTGATTCAGTCCTGTCTCTGATGACCAAGGAGATGTTCAGAGCTAAATTTGGATGTTCTTACTGCTGTTACTTCGGTGTAAATTTCAGTAAAAATAGTATTTAGCTCCCAGTGCTTCTGAGTAATAATTGCTTCAAAATTCTGCTCAGAATTCTTAGCATGCTCATCATTGTGCGTACACAAACTGGAGAATCACAGGCAAAACGCTATTTTTAGGCTGCAAGCTCTTTAGATTGTCCTGGAGCGTGCTGTTTTCTAAGAGATTATTTCATATTTGACAG
Seq C2 exon
AATATGGCGGAAAAATTTCTTGATGGTGAAATCCCACTGGATTCCTTCATTGATGAGTACCAGAGCAAGCGTAAGCTGGCTCACCTGCGACGGGTGAAAATTGAGAAGCTCCAAGAGATGGTGCTGAAGGGACAGAGACTTCCGCTGGCACAGCCTCAGTTGAGGGCAGCCGATCCAACGCCAGCACCTCCAGATTCCTACACTTCGGATGCAAACCCTCCTCCTTCAGCTGTGCCCCGACGAATACCTCCCCCTCCGCCTTCGGTCCCAGCAGGACGCTTTCCTACTCCGTTTACTGCAGCCGTGAGTTCAGGTCCAGCTGTTTCTTATCCAGGTGCTCCGTATCCTCCTCTCCCACCTCGAGCCGGAGCTCAGGCTGCAACTCAGTTGCCACAGCCAGGATGCCCATCTCAGTTTGTACCACAGTATCCTCCAGCTCTTCCCCAAAGACCGCCTCGCTTTCCACCACATCCTGGTTTTATTCTCCAGTGAATATTTTGGTGCGCCTGACTTACGTATTGGTGCTTATCGTTCCTTTTTCTCCCCCTGTCAGAGACTTAATGTAGGCAGTGGAAAGCCTCTGTTTTTTGCACAATGGAGTATAAAATTTGAGCTCTGGCACAGAGGTTTGAAATTGTGTCTGGTGGATATTATTGTTTTCAAATATCAATGACAACGAGGATTTTCTAGGAAGGTGGTAAGGGCTAGATGTGCAAGAGTGCACAGTGGATTTCCTGACGTTATAAATCTCTGAATTCTTTAGTGATGGCAGATCAGTGTCCTGTTCTGTTCTGATGTGTTCCTATTGCAGCTGGATGTATGTGTGGCAAACCAGGAGCTGTTTGTCTCCCTAAAGAATTCTGTCAGTGCCAGTGTTTGTATGGTAACAGCCATATCTGAACTCTGGGTGAGGAGTTCTAATGGACCTCAGTAGCAGCTTTTGTAGTGCACCCACGCTGTGGCAGGTCTGGCCAGGTGCACAGTGAGCTCACTGAGGTGAAACTGTTGTCGGATAAAGTTCTTTTTAAATATTGAAAGTTACAAGAGTTTTGTTTCTACATTTCAGTTGTTACCTTAGACTTTTCATAATAAAAGTACACACTCTTCCCGTTCCTGAATAGCTGGTATCCTGAGAGTCCTGGTCTCTTGAAATTTAACTAAGCTGTTTGTACAGCCAGTTCAGACTTTTATAGAGACTTTAACAGGCATTTTTATTTCTTTACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003743:ENSGALT00000005939:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.761
Domain overlap (PFAM):
C1:
PF072008=Mod_r=FE(18.0=100)
A:
NA
C2:
PF072008=Mod_r=PD(24.0=22.0)
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:
CCTTCAGACTGAGGGGGCTAA
R:
CGGCTGCAGTAAACGGAGTAG
Band lengths:
344-1477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]