BtaINT0140369 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11126814-11128656:+
Coord C1 exon
chr3:11126814-11126924
Coord A exon
chr3:11126925-11128578
Coord C2 exon
chr3:11128579-11128656
Length
1654 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGA
5' ss Score
5.96
3' ss Seq
TTTTGTTTTTTTTCCCCCAGACC
3' ss Score
12.16
Exon sequences
Seq C1 exon
GCCTTCCTGGAAAACGAGGATCTCGGAAATTCACTGGGCAGTGTAGAAGCCCTTCTTCAGAAGCATGATGACTTTGAGGAAGCTTTTACTGCCCAGGAGGAGAAGATCACA
Seq A exon
GTAAGAAATGGGCCCTTGTTTGGGCATTGGCTTCATTTTTTTTTTTTTTAACTTTACAATATTGTATTGGTTTTGCCATATATCAAAATGAATCAGCCACAGATATACATGTTAATTGGAGGATAATTGCTTTACAATGTTGAGCTGGTTTCTGCCTTACAACAATGTTATTCAGGGAATGTATATATACATTCCCTCCCTCTTGAACCTCCTTCCCATTCCCCACCCAATCCCACACCTCTAGATTGTCACACAGCACCAGGTTGAACTCCCTGTGTTTCACACATCTCATAGATTACCAATTCTTAGAATTACTCATAACTATCAGACATGAGAGTTGTTTTAAAAAGAGAAAACATTCAGAAAAATAATCATACCCACTTTTTATCAACACATTTCTTATTCCACAAAGCATATTTAGAAAGTATTTACTTTTAAATTTTTTTCAGAATTAGGTAAATTTATTTTTTAATTAATTTAATTGTAGGACAGTTCCTTTAAAATATTGTGATTTTTTTAGAAAGTTTTTAAAGATTTTGAGCAATTTATATTTTCTGACACAGTGCCTGATTGTCTTATTTTTTTTTCCTGAAGTATAAATAGAAACTATGGGATCCATATCCAATATGAATCATAACTTAACATATATTTGAATGTATTATTTACATTTTTTAGTCTTTTCCTCTCCAGTAATATCTCCATTTAGCTTTCTTTAGTAATATCTAGATATCTAGGTAGTATCTATTTTTTCCTGTATATCTTCATCTTTACGTTTTGCATTTAATGCTGCTATAATTTTCTTGTGAACCTTAAGTTACAGTGTCCCAGAAACTTGTCAATACATAAGCAAGTCTCAGAGAAGTGTAAGGGAGACTTTATTTGCCCAATATATATGTACTGTATGTCTTCGGCTGTCTCCTAGGACTGTGCTGGGGTTAGCCAAAACTTGCACATGTGCATGTATACCACCAGCAACAACAATAACCACAAAACTCCAAATTTTCTTTGTTAATCTTAGATCAATTCAGAGCTTGCTATGGTCCCTTCCCAGTTCATATGCTTATTAGGTTGATTTTCATTGGTAAAAGATAACAATGTAAAATAAGTTATTGTTTATTAAATACTATTTGTAATTTCACATCATTTTCCTATTCCCAATCAATTAATTCATCCTGAGCAATTTTGAGAGTTTATGAATGAATATGAGTCAAAATTCACATGTATAATATGACTCCATTCCCCATATAGCTAGAGATAGAGATGAATTATTAAGAAGTACATATGGTATATGATGGATGGGTGAGTGAATAGATAGATAGATAGATAAATACTGGCCATTGAACAAGGCTGTATCAACAATGGTTCTTAAAAATTTTAAAATAGATCAAATACTCACCTCATAGTGAAAACAGGTTTCATTCACTGTAACCTAGATTAAGAAGAAACTACTGTGGCATAGAGAAAATAATTAACCTGAGATTTATATTTTGAAATACAATTTATAACAGAAATCAGAAGTAGGACCCAGATCTTCTGACCCTGAATCTTGTCCTCTTCCCACATTGTCATGCTTCTTCTTTAAACAGCTAAACAAACTGTGGCGACTTACTCAGTGCCAATGAGAGAAAAACACTTTTTGTTTTTTTTCCCCCAG
Seq C2 exon
ACCATAGACAAGACTGCAACCAAACTGATTGATGATAAGCATTATGATTCAGAGGAGATCGCTGCTATCCGGGATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:12
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(34.3=100)
A:
NA
C2:
PF0043516=Spectrin=FE(23.8=100)
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:
GCCTTCCTGGAAAACGAGGAT
R:
CGGATAGCAGCGATCTCCTCT
Band lengths:
182-1836
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]