GgaINT0124383 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5174344-5175456:+
Coord C1 exon
chr17:5174344-5174552
Coord A exon
chr17:5174553-5175335
Coord C2 exon
chr17:5175336-5175456
Length
783 bp
Sequences
Splice sites
5' ss Seq
CAAGTGTGT
5' ss Score
3.84
3' ss Seq
TTCTTCTCTCATGATTTTAGAGA
3' ss Score
7.97
Exon sequences
Seq C1 exon
GATCGGCTGAAGGACCTGAACAGCCAGGCTGACAGTTTGATGACCAGCAGTGCTTTCGATACCTCCCAAGTAAAGGATAAACGTGAAACTATAAATGGGCGCTTCCAGAGAATCAAGAGCATGGCAGCTGCCCGCCGTGCGAAGCTCAACGAGTCGCACCGCTTGCATCAGTTCTTCCGTGACATGGATGATGAGGAGTCCTGGATCAA
Seq A exon
GTGTGTATTTTGGAAGTTTGAGGCTCTGGCATGAGGGCATGATGTGCTTACTGTCAGCTTGCCAGCAGTGTTCGGTCTGTAGTATGGTTTTATAACACAAGTATGGGTCTCCACAAGAAGTCACCTTTGCCTTCTAGTCAAGGAAAACTATATTCAAAATGACTTCTGCTCCAGTTTGGGTGTGGCTTCTTATCTACAGTGCTCTGTGGTCTGACTCCAGGAGGGAAAGGTCTGTGCTGGAAGAAGTAGCACTCTTTAGCCTTGAACCAGATAACTGCAATTTGACTAATCCTTTTTGGGAAAGCTCACAGAAGAAGTTCGGACCTTACTTTTTCAGTCTGAAGTAATGCTCTTGTTGTTCTAGCCAATGGTAGTAATGAACCTAATGTCCTTTCCACATTGGTGTTAATACCCTGAAGGAAGTGAACTTCATAGAAATCATTCAGATTAGACTGATTCTTTTGTCTTGCTTGTAGAAAATGAAAAATAGTGATTGGACAACAGCAGGTAAACTTCTTGAAGTGCAGCTATCTTAGAAAACAATGCAGATAAGCTGTCCTTCATAGAGAAATGATAGACCCTCTGCCTTCCCTTTCTTCTCCCTATCCATTCCCGTTGTGTGTCAGGAGCCAGCTGCTGTTTGACAATAGCTCATACACAACACAAAGACTTTGGTGTTGTGAAGAGCATTTCCTTATTTGCAATGTTGATTTTTTTTCTTTTATAAGATTTGATCTATGTAAGTAATTTTCAAATTTTCTATTTCTTCTCTCATGATTTTAG
Seq C2 exon
AGAGAAGAAACTGTTGGTGAGCTCAGAGGACTATGGCAGAGACCTGACTGGTGTGCAGAACCTGAGGAAGAAACATAAGCGCTTGGAAGCAGAATTAGCTGCCCATGAACCTGCTATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.086 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(47.6=71.4),PF0043516=Spectrin=PU(16.2=24.3)
A:
NA
C2:
PF0043516=Spectrin=FE(38.1=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:
GATCGGCTGAAGGACCTGAAC
R:
GGATAGCAGGTTCATGGGCAG
Band lengths:
328-1111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]