GgaINT0124356 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5156777-5157464:+
Coord C1 exon
chr17:5156777-5156932
Coord A exon
chr17:5156933-5157259
Coord C2 exon
chr17:5157260-5157464
Length
327 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TTTTCTTTCTTTGTCTGTAGGAT
3' ss Score
12.87
Exon sequences
Seq C1 exon
CTTCTGAGTCGCCGAAATGCTCTTCATGAAAGAGCCATGAAGCGCCGTGCCCAACTGGCAGACTCTTTCCATCTCCAGCAGTTTTTCAGGGACTCTGATGAACTGAAGAGTTGGGTTAATGAAAAAATGAAAACTGCTACCGATGAGGCTTACAAG
Seq A exon
GTAAAAACAAAGATCAGTGTCGGGGTATTTTTAAGGCAATACCAAGCTTAATATAATCAGTATAATGTTATGAAGCGGGATCAGACAGATCTTGCTGAAGCAGGCAGTATTAACGGGAACAGGAAGAACTGCAGTTTCTCCCTGTGGTGCTGTAATCATGCTAATCCAATAGCTTAAATGTTCTGATTTCAAAGGTGTATTTGTGGCACCAATTCCTCTTGTGGCATATTGGCACGTATATAAGTGTAGTTGAATTTAAAAATGTCTTCTGAGATCTCCAGATATTAATTCTGGATTGAAAGTTTATTTTTCTTTCTTTGTCTGTAG
Seq C2 exon
GATCCATCCAACTTGCAAGGTAAAGTTCAGAAGCATCAGGCTTTTGAAGCAGAGCTTTCTGCTAATCAGAGTCGTATTGATGCACTGGAGAAAGCTGGCCAGAAGTTGATTGATGTCAATCACTATGCATCTGATGAGGTGGCAGCTCGCATGAATGAAGTCATCAGCTTGTGGAAGAAACTTCTGGAAGCCACCGAGCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.135 A=NA C2=0.159
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
A:
NA
C2:
PF0043516=Spectrin=FE(65.4=100)
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:
GAGTCGCCGAAATGCTCTTCA
R:
CGGTGGCTTCCAGAAGTTTCT
Band lengths:
347-674
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]