GgaINT0124348 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5151955-5152945:+
Coord C1 exon
chr17:5151955-5152088
Coord A exon
chr17:5152089-5152800
Coord C2 exon
chr17:5152801-5152945
Length
712 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
ATTTGTGCTTTGTTTTGAAGGGA
3' ss Score
8.15
Exon sequences
Seq C1 exon
GAACAGCACCCTGAGGAGGAACTTATAAAGTCCAAACAGGATGAAGTAAATGCAAGCTGGCAGCGTCTTAAGGGGCTTGCCCAACAGAGGCAAGGAAAACTCTTTGGGGCAGCTGAAGTTCAGCGCTTCAACAG
Seq A exon
GTATGATCCTGGCTGGATCTGCTGTAGTGATGTCGTTCTGTATATAGATGTCTGATGATCCTTTTATCTACATACAGTATTGTGAGAAGGGCTACCACTCTCTGGTTTTGTTTTACTCTTCCTCATGACTGAGGAACTTGTTCAAAGGGAATTCTGAAACAGTCATTCTGTTCTAGGTTTTCAACACCTGGAAATTCTGTTCATTCTTTTGCATGGCAGTTCTCCCAGTCTTTACTCTGAGAGCTTCCCTCTCTTCTATCCCACATGAGCCTTTAAAGAAGTGGTTTTTCTTTGTTGTTGCTGGCTAGATGTCAGTCCAGTTGTTCAGGGCAGGAAGGGGGGTTGTGGGGGGTTGTCTTTGAGCACTGTCTTTCTATCTTATCTGCTGCTTGTTATTTTGAGGTTTGCTATAATGAAGTTGGAGAGGGGTCTAGGGTAGAAAACTGACTGATGGTGCTATAATTCCTTATTTCCATTTGGTGAGAGCATCTGAAGAATGGCCTGCCAACACACTTGAATGCTTTGGGGGATAAAAAAACATGTGTAGACATCTTTTCAGGTGCTTTTGGTTTGTTAGTTTTTTATTGTCATCAGCTACAGTGTTTATATATGACTTTGCACTGCAAGTACGCCTGTAATAAGTGAAAACATTCTGCTTTCTTCCCCTTTCCTTAAAAGATTTACTACTTCCAATTTGTGCTTTGTTTTGAAG
Seq C2 exon
GGATGTGGATGAAACTATCAGCTGGATTAAGGAGAAAGGGCAGTTGATGGCCTCAGATGACTTTGGCAGAGACTTGGCCAGCGTGCAAGCTTTACTACGTAAGCATGAAGGCCTGGAAAGAGATCTTGCAGCTTTGGAGGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(32.7=75.6),PF0043516=Spectrin=PU(6.7=15.6)
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:
GAACAGCACCCTGAGGAGGAA
R:
CTTATCCTCCAAAGCTGCAAGA
Band lengths:
279-991
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]