BtaINT0140386 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11174739-11175150:+
Coord C1 exon
chr3:11174739-11174838
Coord A exon
chr3:11174839-11174952
Coord C2 exon
chr3:11174953-11175150
Length
114 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
CTGATCCCTTTTTACCACAGGAG
3' ss Score
8.67
Exon sequences
Seq C1 exon
GGACTTACAGAATTGGATTAGTGGCATTGGTGGCATGGTTTCATCCCAGGAACTGGCTGAAGATTTAACTGGCACAGAGATCATGATAGAGCGGCATCAG
Seq A exon
GTATGGTGACAAAAGCCTTAGCCTCTGATCACATAACCTCGCAAACTTCCTGCATTTTGCAACTTTTGTGAGATGTCACTGGACTCACCAGTCTCTGATCCCTTTTTACCACAG
Seq C2 exon
GAGCATCGTGCTGACATGGAGGCCCAGGCTCCCGCCTTCCAGGCCTTTGAAGATTTTGGTACAGATCTTACAATCAGTGGGCACCGGGCCAGCCCCGAAATTGAAGAAAAGCTTCAAGCTGTTAGACTAGAGAGAGATGAGTTGGAGAGTGCTTGGGAACAACGCAAAAAGATGCTAGATCAGTGTCTGGAGTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.294 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(31.4=100)
A:
NA
C2:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
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:
TTGGTGGCATGGTTTCATCCC
R:
TTTTGCGTTGTTCCCAAGCAC
Band lengths:
243-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]