GgaINT0124375 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5169435-5169900:+
Coord C1 exon
chr17:5169435-5169632
Coord A exon
chr17:5169633-5169753
Coord C2 exon
chr17:5169754-5169900
Length
121 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
TTGGAGTTTTTCCTCTTTAGCTG
3' ss Score
5.85
Exon sequences
Seq C1 exon
GAGCACCGTACTGAAATAGATGCACGGGCTGGCACTTTTCAGGCATTTGAACAGTTTGGACAGCAGCTTCTGGCTCGTGGACACTATGCCAGCCCAGAGATTAAGGAGAAACTGGATATTCTAGATCAAGAACGGACAGACCTAGAGAAGGCCTGGGTCCAGCGCAGAATGATGCTAGACCAGTGCTTAGAACTACAG
Seq A exon
GTACTCTGCTGCATTTTTAAAAAGAAAGATAATTTCTTCTTTCATAAAAATGCCTTCATTCACAATGATGAGGGATGTTCTCGGTCTGTCTTCCTCATGCTTTGGAGTTTTTCCTCTTTAG
Seq C2 exon
CTGTTTCATCGGGATTGTGAACAAGCTGAAAACTGGATGGCTGCCCGAGAGGCGTTCCTAAATACAGAAGACAAAGGAGACTCCTTAGACAGCGTGGAGGCACTCATCAAGAAGCATGAAGATTTCGATAAAGCAATCAATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.7=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:
AGTTTGGACAGCAGCTTCTGG
R:
CCTCCACGCTGTCTAAGGAGT
Band lengths:
246-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]