GgaINT0124390 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5177526-5178299:+
Coord C1 exon
chr17:5177526-5177735
Coord A exon
chr17:5177736-5178002
Coord C2 exon
chr17:5178003-5178299
Length
267 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GTTTATTTTCTCTTTTCAAGGTT
3' ss Score
10.43
Exon sequences
Seq C1 exon
GAAACCTTTGATGCTGGACTTCAGGCTTTCCAGCAGGAGGGAATTGCAAACATCACTGCTCTGAAAGACCAGCTACTGGCAGCCAAACATATCCAATCAAAGGCCATTGAGGTTCGTCACGCTTCCTTGATGAAACGCTGGAATCAGCTGCTTGCTAATTCTGCAGCCAGGAAAAAGAAACTCTTGGAGGCTCAGGAGCACTTCAGAAAG
Seq A exon
GTGAGTCACCAAACCACAGGGCTACAAAAATCTCATTGTTCTCTTTGGAAGAAAAACAGTACAACAGTTGGCACTTAGGCAGCTTTCTTATTTGCAGCTAATGATTATGGAGATCCAGAGGACTTGAAAGTTTTTGATATACTGGCAAGAAATGAGTAATAGAGGCAAACTATTTTTTGAGCTTGTTAACTTTAAATAATCTCATACAGAATATTTGTATTAACGGCGCAACGGAATTGAACAACCAGTTTATTTTCTCTTTTCAAG
Seq C2 exon
GTTGAAGATCTCTTCTTGACTTTTGCCAAGAAGGCCTCTGCCTTCAACAGTTGGTTTGAGAATGCTGAGGAGGACCTGACGGATCCCGTGCGCTGCAATTCCCTGGAAGAAATCAAAGCACTGCGAGAAGCCCACGATGCGTTCCGTTCCTCACTTAGCTCTGCCCAAGCTGACTTCAACCAGCTGGCAGAGCTTGATCGGCAGATCAAGAGCTTCCGTGTAGCCTCCAACCCGTACACTTGGTTTACTATGGAGGCTCTTGAAGAAACTTGGAGGAATCTGCAGAAAATTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(58.5=88.6)
A:
NA
C2:
PF0043516=Spectrin=PU(91.4=97.0)
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:
GGTTCGTCACGCTTCCTTGAT
R:
CTCTGCCAGCTGGTTGAAGTC
Band lengths:
292-559
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]