BtaINT0140370 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11128579-11128943:+
Coord C1 exon
chr3:11128579-11128656
Coord A exon
chr3:11128657-11128787
Coord C2 exon
chr3:11128788-11128943
Length
131 bp
Sequences
Splice sites
5' ss Seq
GAAGTATGT
5' ss Score
6.97
3' ss Seq
TTTGTTTATGTTTTTTGCAGCTG
3' ss Score
10.2
Exon sequences
Seq C1 exon
ACCATAGACAAGACTGCAACCAAACTGATTGATGATAAGCATTATGATTCAGAGGAGATCGCTGCTATCCGGGATGAA
Seq A exon
GTATGTGCATCTGCCTGCCTGTGCACCCGGGCCAGGGAAAATGTTGGAGCATTGTTAACCATGGTAGGCAGTAGATCTCAGGCATCCATATTTTATTTTTCTGACCGTGAGTTTGTTTATGTTTTTTGCAG
Seq C2 exon
CTGTTGGTCCGACGGGACAATCTACGAAAAAGGGCTGCCATTAGACGCGGATTGCTGGAGGATTCATTCCTTCTGCAGCAACTGTATCAGGACTCAGATGACCTAAAGAACTGGATCAACAAAAAGAAAAAGTTGGCAGATGATGAAGATTATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:13
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=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(23.8=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCATAGACAAGACTGCAACCA
R:
CTTATAATCTTCATCATCTGCCAACT
Band lengths:
234-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]