GgaINT0124362 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5160340-5160961:+
Coord C1 exon
chr17:5160340-5160432
Coord A exon
chr17:5160433-5160826
Coord C2 exon
chr17:5160827-5160961
Length
394 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TCTGTTCCTTCTTTGTTAAGCAA
3' ss Score
6.25
Exon sequences
Seq C1 exon
GCTCTCCTGAAGAAGCATGAAGCTTTGATGTCTGATCTTTCTGCTTACGGCAGTAGCATACAGGCATTAAGGGAACAGGCCCAGTCCTGCAGG
Seq A exon
GTAAGGAAGGATGCTAATCATGTTGCTGAAATTCTTGGGTCAGCAGAAGTTAAAGACCAAGCTTAATAGCAGCTGTTGCTTTTGAGAACTTACTGCAGACTGCACTTAATTTTCTAATTAAAAAAAGTATATATAGTTATCTTTTTATAATTGTAACAAACTGCTGTGTTACATTGGAAGAAAACAGAGCAATGTGATCGTTTCCAACGTTTGAGCCCAGAGAGTGCCTAAAATGAGTCCATCTGTGCTACATTTATTTCAACAGGAATCACTTTAGAGCATTTACAGTACCTTTAAGGCTGAAGTGTTTTTCAGGATCGCTACTTTGGTTGTAATAACCATACAAAAGTTTCTGCATCTTTACTCATTTTTCTTCTGTTCCTTCTTTGTTAAG
Seq C2 exon
CAACAAGTTGCTCCCACTGATGATGAAACTGGAAAAGAGCTTGTGCTAGCACTCTATGATTACCAAGAGAAGAGTCCTCGGGAGGTGACTATGAAGAAAGGAGATATTCTAACCCTGCTCAACAGCACCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.156
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(35.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(17.9=33.3),PF0001823=SH3_1=PU(63.0=64.4)
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:
GCTCTCCTGAAGAAGCATGAAGC
R:
CTTGTTGGTGCTGTTGAGC
Band lengths:
228-622
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]