GgaINT0124365 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5162818-5164289:+
Coord C1 exon
chr17:5162818-5162877
Coord A exon
chr17:5162878-5164090
Coord C2 exon
chr17:5164091-5164289
Length
1213 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
TCCTTTTCTGCTTGTTCCAGGTA
3' ss Score
11.05
Exon sequences
Seq C1 exon
GACTCTCATTACTAAGGAAGTCGGCAGTGTATCTCTGCGTATGAAACAGGTCGAAGAACT
Seq A exon
GTGAGTAGGATTAGCCCTTTCTAAACCATGCTGTCTCCATACTGTCACTGTTCATTCTCTTTGTTTCTTTCTTTCTTTGGGAAAGCTGCTCCGAAGAGACACGAAGGAAGCAATTTCTGCCATGTGTGTTATTTTAGTTTAGATGAATGTGTCGTGATGTGCGTTTCGTGTGTTGTGTACAGCCAGCCATCCTGCCAGCTGCTTATCTTGTTGGTCACGTCAGCACTGCTAGACTGGTGATGGTGTCATTTTCCATTGTACTGATTTTACTTGCCAAGTGAGGGTTCAGTGATACCTACGCTGTTCTCTTTAAAAAGCGTATGTTGCATTTTCTGAGGTGCAGATACAATTACTTGTTCGTATAAATAAATATACACGGTGTATCTGTTTTATACTTAACATCACATAAATGTCTGCTTCTGGTGGAATCTTGCCCCAGGTCCTCTTATGAGCTCTGCAAGTACTCCGTACCTAAAACTGTATGCTGAAGCAAACATCTGCAGTTGAGTCAGGCTTTAAAAAAGTGTTTTCCTACAGGCAGTAGTTCATGCAAGTCAGACTAGAATGCTGCCATTTAATACAAAAGGTTCTTGGTTCCTTATATCCAGTGTTGAATTCAGGATAGATGGAAAACCACAGTGTCTCAGGCTAGAGACTTTTCTGAGCACAGGTTCTTTGAAAATGGACATTTGGATTGCCAGGAATTGAACAGGAGACATCAGATTTTGTGCTTTTAAATACAATGATGCTGCTGTATTTTCACATTGGTCTTTCACGATTTAGTTGCTTGTTCAAGCCAATTTAAGCACTTCAGAATAAATGTGAAGTAAAACCTCTAAGGTAAATGAGGAATATTTTCACTGATACCATTGGTAATTCTACAGATATGTACAAACAGCGCATGTAAAACAAATTCAATGTGTCCTTCCTGCACTGCAGTGCTGCTGCAGCCTTGAGCTGTGATTTGGATTTGCCTTTATCTACTGAAGCATTGCATGTGGGAGGTCTCATTTTAGTGTGCTTACCCATATAAAGGAGGCACGTGCACAGTTTGCATTGAGCTGATCATGAACAACTACGTCATTCTGTAGAGTAGCAGCGTGCAGATTGCAGGCACTTCCAGCATCTTTGGTGCTACCTGAACTTGCCTAATGACTGTGACTCTGCTCAGTTCAATCTGACTGCTCCTGCCTTCCTTTTCTGCTTGTTCCAG
Seq C2 exon
GTATCATTCCCTTCTTGAGCTGGGAGAAAAACGTAAAGGCATGCTAGAAAAAAGCTGCAAGAAGTTTATGCTTTTCCGTGAGGCTAATGAGCTTCAACAGTGGATCAATGAGAAGGAAGCTGCGCTCACTAATGAGGAAGTGGGTGCTGATTTGGAGCAGGTGGAGGTGCTACAGAAGAAGTTTGATGATTTTCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.045
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043516=Spectrin=PU(54.8=68.7)
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:
TCTCATTACTAAGGAAGTCGGCA
R:
TCTGAAAATCATCAAACTTCTTCTGT
Band lengths:
254-1467
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]