GgaINT0124355 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5156526-5156932:+
Coord C1 exon
chr17:5156526-5156603
Coord A exon
chr17:5156604-5156776
Coord C2 exon
chr17:5156777-5156932
Length
173 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
CTTTTCTTTTATTTGTTCAGCTT
3' ss Score
8.43
Exon sequences
Seq C1 exon
GCACTGGATGAGTTTGCTACTAAACTGATTCAAAATAACCATTATGCCATGGATGACGTTGCTACGCGCAGAGATGCT
Seq A exon
GTAAGTATCCAACACAGATTTAGACTGCAGGTTTTCTACTTTATTATTTTAAATAGTATGGCTACAATATGGGATAAATCACTGGAGGTTTCAATGCATACAGCAGACTTTCTTATAAACTGAAGAACTTAAAAATCTTCACTTACGTTTTTTCTTTTCTTTTATTTGTTCAG
Seq C2 exon
CTTCTGAGTCGCCGAAATGCTCTTCATGAAAGAGCCATGAAGCGCCGTGCCCAACTGGCAGACTCTTTCCATCTCCAGCAGTTTTTCAGGGACTCTGATGAACTGAAGAGTTGGGTTAATGAAAAAATGAAAACTGCTACCGATGAGGCTTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:13
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=0.135
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(23.8=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
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:
GCACTGGATGAGTTTGCTACT
R:
CTTGTAAGCCTCATCGGTAGCA
Band lengths:
234-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]