BtaINT0140412 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11203289-11204434:+
Coord C1 exon
chr3:11203289-11203433
Coord A exon
chr3:11203434-11203974
Coord C2 exon
chr3:11203975-11204434
Length
541 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
TTTTTCTTTTAATGTTTCAGGCC
3' ss Score
11
Exon sequences
Seq C1 exon
AAAGGGCTATATCTCAAAAGATGAGTACATCGACTTCTTGACTGACAAGGAGTCAGAGAACATCAGATCCAGTGATGAACTAGAAGATTCTTTCCAAGCCCTGGCAGAGGGCAAAGCCTATATTACAAAAGAGGACATGAAGCAG
Seq A exon
GTCAGATTCCCATTTCTATCCACTCTCACTGCACTCTTATAATCATCTAGATTTTGTTCATCTCAGGTCTGGCTCCCTAGTTACTATAGGCAATTACTTTCCTCTTCCCCATATTTTCTCAGATATTGTCATGCACTGGTTATCATTTGCTTTGGTCACTACCTCATGTTGTTTTGACCCAACTCAAAAACCTATAGTCAATATCTAATTATTTCATCATTAATCCCAAGCATGCTACTTGGTTTTAAGACTATTTCTTTATTCTGTTTATTTAATAAGCCAAATTTAAAGAAGGGGGTAAACAGTGCAATCAGAATGAAATGGGAGTCTTTGGATAAGAACTGAGTTGAAAAGATGAGTTGGTCTTATTCATTAGAAATTACAGATTTCTTTCTATAAGAAAAGCACGTGATAGGCCTGGGACCAACTGCTTTTGCCCAAACCTCTCTACTTCCTGAGTTTAGGGCATATTAGAAGCCCAAAGGAACCAGCTATTCTGAATTTCTGTCACAATAATTTTTTTTTTCTTTTAATGTTTCAG
Seq C2 exon
GCCCTAACCCCAGAACAAGTGTCATTCTGTGCCTCACGTATGCAGCAATATGTGGATCCCCGGGGCCGAAGCCAACCTGCTGGCTATGATTACGTTGGCTTCATCAATTCTTACTTTGGCAAATAAAAGACAGCTTTTTCTGGGTCAGAGAACCTTGATGTTGTGGGAAGTATTGGGGGATGAAGGAAATAGGCAGATATGGAAGATGGGAAGACAGTTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTTACATTTATTGTAGGACCTGAAAAAAGAAATCTCGAGCTTGAGAGATAAAGGCATTAATGACATCAGAGGAGAGGAGGCTATGGGTTTATTTTATATGCAACTATCACTGCTGAAGGGTGTTAGGCAAAGTTTCTATTTTTCATTTGTTGGGTTCTATGTAATATTACTTTATTTTGTTCTGATTATAGAATAAAGTATTTCTTTTTTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:51
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.163 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(14.6=26.5),PF087265=EFhand_Ca_insen=PU(40.6=57.1)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(56.5=92.9)
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:
CTTTCCAAGCCCTGGCAGAG
R:
GCCTTTATCTCTCAAGCTCGAGA
Band lengths:
358-899
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]