GgaINT0124388 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5176891-5177366:+
Coord C1 exon
chr17:5176891-5177050
Coord A exon
chr17:5177051-5177289
Coord C2 exon
chr17:5177290-5177366
Length
239 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
GAATGTGCTTCATTTTCCAGGTG
3' ss Score
10.57
Exon sequences
Seq C1 exon
AATAATCACCATGTGGAGAACATTACTGCTAAGATGAAGGGCCTCAAGGGCAAGGTATCAGATCTGGAGAAAGCCGCAGCTCAGAGGAAAGCCAAACTGGATGAGAACTCTGCCTTCCTCCAGTTCAACTGGAAAGCAGATGTGGTGGAGTCATGGATAG
Seq A exon
GTATGTTCTATGTTGGAGCACAGCATGCTATCACAAAGAAACTGAAATGCACCTCCATTTCTCAATATCTCATGTAGCTTCTCACTTTCTGTTAGAGTAAGTAGACTTAATACTGCTCATTCCTTTGGGTTTATACCTGATAGATGCTTGTGAGTTAATTGTTAGACCGTAATTTGGAACTGAGGAAGCATTTGAGATGGAGGTGTTTTCATTTTTACTGAATGTGCTTCATTTTCCAG
Seq C2 exon
GTGAGAAGGAAAACAGTCTGAAGACAGATGATTATGGCCGTGACCTCTCCTCTGTGCAAACACTACTCACCAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(32.4=63.0),PF0043516=Spectrin=PU(16.0=31.5)
A:
NA
C2:
PF0043516=Spectrin=FE(23.6=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:
AGAACATTACTGCTAAGATGAAGGGC
R:
TGTTTGGTGAGTAGTGTTTGCAC
Band lengths:
220-459
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]