GgaINT0124374 @ galGal3
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
NA
Coordinates
chr17:5796013-5796444:+
Coord C1 exon
chr17:5796013-5796112
Coord A exon
chr17:5796113-5796246
Coord C2 exon
chr17:5796247-5796444
Length
134 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CAAATCTCTGTACCTTGCAGGAG
3' ss Score
8.09
Exon sequences
Seq C1 exon
AGACCTTATGTCTTGGATCAATGGAATCCGGGGTCTGGTCTCCTCAGATGAACTTGCAAAAGATGTGACTGGAGCTGAAGCTCTGTTGGAAAGGCATCAG
Seq A exon
GTATGTGAAAGGTAGTAAGCGACTATCAAACATCAATAGATGTTTATTTTTCTGACACTTTCCACTTACAGTCCCCAAAATTAATCAGTCACTGCTCTGTCCTTCATTTAATAACAAATCTCTGTACCTTGCAG
Seq C2 exon
GAGCACCGTACTGAAATAGATGCACGGGCTGGCACTTTTCAGGCATTTGAACAGTTTGGACAGCAGCTTCTGGCTCGTGGACACTATGCCAGCCCAGAGATTAAGGAGAAACTGGATATTCTAGATCAAGAACGGACAGACCTAGAGAAGGCCTGGGTCCAGCGCAGAATGATGCTAGACCAGTGCTTAGAACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000007516:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.265 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(31.4=100)
A:
NA
C2:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGTCTGGTCTCCTCAGATG
R:
TAGCATCATTCTGCGCTGGAC
Band lengths:
248-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]