GgaINT0124396 @ galGal4
Intron Retention
Gene
ENSGALG00000004719 | SPTAN1
Description
spectrin alpha chain, non-erythrocytic 1 [Source:RefSeq peptide;Acc:NP_001036003]
Coordinates
chr17:5183006-5183640:+
Coord C1 exon
chr17:5183006-5183202
Coord A exon
chr17:5183203-5183586
Coord C2 exon
chr17:5183587-5183640
Length
384 bp
Sequences
Splice sites
5' ss Seq
TCGGTACGG
5' ss Score
8.77
3' ss Seq
GTTTGCTTCTTCCCTTTCAGAAA
3' ss Score
11.64
Exon sequences
Seq C1 exon
CGCAAGCACCAGGAGATCCGGGCTATGAGGAGCCAGCTGAAGAAGATTGAGGACCTTGGAGCAGCCATGGAAGAGGCACTTATCTTGGACAACAAATACACAGAGCACAGCACCGTGGGGCTGGCGCAGCAGTGGGACCAGCTTGACCAGCTGGGAATGAGAATGCAGCACAATCTGGAACAGCAGATTCAAGCTCG
Seq A exon
GTACGGCCTACCCTGCATGCAGCGTGCGGTGTGCCTGGCTGGGGGGAGGTGAACAATAACACACCACTGTCTGTCTGAAAGCAAACCTTGTGCAGTCCGTGCTGATGAGTCTCTCCTGTGTTCTGCAGAGCAGAGCTCCTTAACCCCCAGCATTTCCTAGCTCTCTTCAGAGGGATGAAGTTAGCATGGTTTGGAATAGTTCCTGCTGGCCATTAGCAGTGATGACTTGGAGGAGCTGATTTATTCCCTCTGAGCTGTGATGATGCGATGTGTTGTCTGCTCACTTGTCCTCAGCTGATGCAGACTGCTGGTTTGGGGCAGATGGACTCCATTGGAGTTCTGCAGTTTAGGAACCGTTCACTAAGTTTGCTTCTTCCCTTTCAG
Seq C2 exon
AAACACAACTGGAGTCACAGAGGAGGCCCTGAAGGAGTTCAGCATGATGTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004719:ENSGALT00000039770:53
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.298 A=NA C2=0.263
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(56.6=90.9)
A:
NA
C2:
PF134991=EF-hand_7=PU(16.0=63.2)
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:
GCAAGCACCAGGAGATCCG
R:
TGAACATCATGCTGAACTCCTTCA
Band lengths:
249-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]