BtaINT0140403 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11195079-11197419:+
Coord C1 exon
chr3:11195079-11195288
Coord A exon
chr3:11195289-11197122
Coord C2 exon
chr3:11197123-11197419
Length
1834 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TTGTCTTTTTTTCTTTATAGACT
3' ss Score
10.38
Exon sequences
Seq C1 exon
GAAACACTGCATGCCAGTCTGCAGAGCTTCCACCAAGAGAGACTGTCTGAGATAACTGACCTGAAGGATAAGCTTGTGGCTGCTGAGCACAGCCAGACGAAAGCCATTGAGGAGCGCCATGCTGCCTTGCTGAGGCGCTGGGAACAGCTGCTGGAAGCCTCTGAAGTCCATAGACAGGAATTGCTAGAGAAACAACGGCCCCTACTGGAG
Seq A exon
GTAAAAAAAAAAAAAAAATGATGCACCATCATCTGACCTTGAATATCTATATCCAGAAACAGATACTGGAAACCATGTTTGAATACTATAGACAATTAAGTGAGTATATTGCAAAGAATCAGGAAGACATTCTTATAAACATGAAGCAATTCATTTTTAGTTTGATAAGTTCTTTTTTTCTTGGACTAATTGATCAGCTGACTTATGATGGAAGTCAGACACATATATTGGAAACAAGTAGGTGAGACAAGGATCTTAATTTAAGGCAGAACTAATACTGGCATATAGGAGTCAAGATTGCTCTTGTGCTTTTTCTAACTCAAATAAAAGGAATATTAGACAAGTAAAATTTGTGTTCTCATCTTTCCTAGCCGGGGGACCTTCTATATGTTGCTTAACATCTCTGAATCTTGATTTCTCTATTTAGAAATCTTGATGGATCTATATCACCATCATATCTTGATGGATCTTGATTACTATCAAAAAAGATAATGGACCTGAAAATGCAATATAAACCACTATGTTCTGTATGGATATAGTTATTAAAATGTTCTTTCTTTTGGTGACTGCTAAGATATTGGATATTGATGATAAAATTATTAATAGTAAAAGGAAGTCAAGATGGTTAGTGAAAATACTGAATACTTCTAGACCATAAAATATTGTACCTGACGACAAGTTAAAGTAGAGAATTAAAGGAATCAGGAAACACACAAATAAAAGTAAGACTCTTAATTTTAACTGTGATAAGGGACATATAACCTACAGAAACTAATCTTCAGTGCAAAATTAAAGCAATTAATGGACAACCACATATTATCTTATTTTGTGATTATAAAATCTCTGTAAAATATTCAGTTGATACATAATATTATGAAAATGTATGACATTATTTATAGGTTTCCATGTCCTTCCAGGGTAGGGGCAGTAATAGTTTTTTCTGTGTTGGTCTATTTTGGTGTGTAGATTGCTGAAATGAATACAGCGACAACATAATGGTATACAATACCTTTGCAATCTCCCTTCCATTTGGGTCAGTTTTTTTCATCTTAACCCATTTTGAGATGAAAACTGATTCTCATATCTGTATAACAAAATCTCTTTGAAAGTACAATCGGCACATATTTATATATGACACAAATTATATGATGTGTTTTAAATCTAAAACTTTGTATTACCTTCTGTTTGGAAAAATCCATACTATTTCTCTTATTTAGAAGTTCACAGTCATTCAGAATGCTCCAGAGAGTATTGCATGGCTAAAGATATAGGTTAGAGGGTAAGAAATGGATTTAAGCAGGGAATTTAGGCATGAGATGAGCTCCGAACAAGGTTTAGAGGAAGGTAGGAAGACAACTCAGTATACACAAATAAACATCAAAGCAGTGAGGGCTGCAGATCACAGAAGAGAAAGAAGAAATGCCTGTCCCACAAATGATTTTTTTAATCTAATCATCCATCCATTCATTCACTTAAACTTAATTCATGCATATTATACTAAAAATTCATGGAACACAGACATCAGAACAAGAAATCATGGAATCTTATTGAAAACTACCTTTGTCACTTTGGGAATCTTATGGCTAAAATAATCCTAGAAGTTACCCAACTTCATTTGTAAGTGTTGGAAGAAAAGAGAAAATGCTTGGATCAGGGCTTGTACCTTGAACTCACATGTCCACCCATCTGATTGCATGGTCTCCATTGGTCTTAGTTCTGTCCTCTTAGAGTATTGGTACAGAAAATATTTGAAGACAGTCATTTTTTTATCCTGTTTTCTTTTCTGCTGATGAACTTTATTGGAAAAGATGGAATTGTCTTTTTTTCTTTATAG
Seq C2 exon
ACTGAGGTTCTATTCATGAAATTTGCACAAGAGGCCTCAGCTTTCAACAATTGGTGTGAGAAGGCCGAGGAGGACCTGTCAGAGCCTGTGCGCTGTGTCTCCCTGGATGCAATCCGGCAGCTGCAGAAGGACCATGAGGCCTTCTTGGCCTCCTTGACAAAGGCCCGAGGAGACTTCAATGATTTGCGAGAGCTAGACCAGCAGATTAAGGCCTTAAATGTGCCCTCCAGCCCCTATACCTGGTTAACAGTGGAGGTGCTAGAGAGAGTCTGGAAACACCTATTGGATACCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:43
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=PD(58.5=88.6)
A:
NA
C2:
PF0043516=Spectrin=PU(91.4=97.0)
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:
AGCCAGACGAAAGCCATTGAG
R:
GGCTGGAGGGCACATTTAAGG
Band lengths:
352-2186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]