BtaINT0140378 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11159590-11161592:+
Coord C1 exon
chr3:11159590-11159682
Coord A exon
chr3:11159683-11161454
Coord C2 exon
chr3:11161455-11161592
Length
1772 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTCTTCCTATTTTTGTTCAGGAA
3' ss Score
9.67
Exon sequences
Seq C1 exon
GCTCTTCTAAAGAAGCATGAGGCCTTTCTAGTGGATCTGAAGGCTTTTGGAAACAGTATGCAAGCTCTTCGGGATCAGGCAGAAGCCTGCCAG
Seq A exon
GTAAGAAGGACTTAAGTATAACAAGAATCACTTTCTCCACTGCAGAGGAAAAGGAATTGTCACCAGTTTTTACTTTACATATTCTAGGAAGCAATTGCATCAGAAAATACTGTCTTGTAATCTTTAGGCAGGCACTGTAGCATCTTTGTAGCATTTACAGAGATTCAGAGCAAAAGAATTTCTCAATAAGTGTTATAATTTGTTCATTGGTATATTTTTGTTTCCTTTTTCCTTTTATATTTCCATTTTCTTTTCTTTTACTTCTTTTATTCATATCTCTCCTTTTTATGTTCCTTCCTTTCTTAGTTATTTTTTATACCAACATGTATTAAATGTCTACCATGTGCAAGCATGAATAAAAGAATAATTCTGACTTGAAGGAAAGTTACAGTCTATTAGGTCATGAATTGTAACAAATAACATATGATAGATACATGAATGGGAAAACAGTCTCAAAGAAAGAAGTGTTTCATTCTCTTGATATTAGAATGCTGGAGGATAGGAAAATCTTCATAGCTGAGGCAAGTCAGTTTATCTGAATTCGTTTTGTAAGGGTGGTTTACTATGCAGATAAGGAGAAGATGGGTTTTTCTAGTGAACAATCTATACGAGCAAATGCTCTGAAGCACAAAATAATCAAGAGTATTGTGAGAATGGCAAGACTGCAAGGTGAAAATAAGTGTCTGGAAGAGTGATGGAAGCAGAAATCAACTAAATGATATGGATGTTTCCTGAGTAGAGTGGAAAGAAAAAAGACACACTTTCACATTCAAGAAATTCTTTCTTATGAGGGGCTCTGAACCCATACACTGCAAGTAGAAAATACATAGGCTTAGAAAGAAAGAAAGTGAAGTCGCTCAGTCATGTCCGACTCTTTGCGACTCCATGGACTGTAGCCTACCAGGCTCCTCCCTCCATGGGATTCTCCAGGCAAAAGTACTGGAGTGGGTTGCCAGGCTTACTATGACAATAAGTATTTACAGAGTTTTAGTGCTGTGCCTTCCTCAAGCTCTGCACAGTAGGTGCCTACATAAAAACAGGTGGATTTATGAATTGTAAGTTATGAGGAAATAGTACTTGAAGGATACAAAATCAGAGGGATATATAAGGGGAGGTATATCTTCACATCCCATCTGAAAAAGATGTGGGTCATTACTTATGAAGGGTGATTATATTTGTTCATTCTCTCAGAGATAAGATATCTGGGGGAAATGAAAATCAGAAAGACTGTATCATGGAGGGCAGGTTTCTTGCTAAAAAGAGAAACAAGATATTTGATCTAGGTTTATTTTCTCAAATATTAAAATTCTAGGCCCTCCCTGTGCTGTCGGCCATTCATCTCTTAAAAAAAAAAAAAAAAGTCCATATTTGGTCTACAAAATACTTTAAAGACCTAGGGAATGGAGAAGGTAATGAAAGAAGTGGATCTTTCACTTTCTCAATTTTCTGAAACATGGATTCATGCAATCCTTTAATATCTGCTTAAGACTGGTGACTTAGAGCATTTAATATGTTTTTGACAAATTAAATTCTTACTTGCTCACTCTATATACATATTTCCCAGTCTGCCTGTCCCCTGAGAAGTGCTAAGATGAAATGATATTTCTAAAGATATCATATTGCAATAGCTCTGTTACTGGCATCCAGGTAAGAGGTTGTAACCAGGAGCTCCTCTCTCCTTTGGGTACAGGAACCTACCCACTGTGGGTAGGTTGTACTGAAAGATCTTTCCTATGGGTGACTAGAATGTTCTTCTTCCTATTTTTGTTCAG
Seq C2 exon
GAACAACAAGCTGCACCTGTGGAGGTGGCTGCTCCAGAAGAGAGGGTTGTGGCCTTATATGACTTTGAGGCCCGCTGCTCCCGAGAAGTCACCATGAAGAAAGATGATGTCTTAACACTGCTCAGTTCCATCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(33.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(22.5=43.5),PF0001823=SH3_1=PU(63.0=63.0)
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:
AAAGAAGCATGAGGCCTTTCT
R:
TTGCTGATGGAACTGAGCAGT
Band lengths:
222-1994
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]