BtaINT0140407 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11200023-11201615:+
Coord C1 exon
chr3:11200023-11200074
Coord A exon
chr3:11200075-11201427
Coord C2 exon
chr3:11201428-11201615
Length
1353 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTCTTTGTCTTTTTCCAGAGG
3' ss Score
10.62
Exon sequences
Seq C1 exon
ATCTTTGCTGAAAGAAACAGGAACACTAGAATCCCAGCTGGAAGCAAATAAA
Seq A exon
GTAAGTAATGTTTATTCATTAGTTCTAAATATTGCTGGAATTTACAGGAGTTCAAGAACTACTCAAAGGAAACTGGTGATTCCTTTAGGTAAATCCCTGGCCTAAAAGTCAAAAGCCTAAGGCTCCGTTGTCAATCTTGCCAACAATTTGCATTCTAACCTTTGGCCACCACTTCATGGACATGGATGTCAGTTTGCTTAAATCTCAACTTTAATTTCTGTATCTACACAATGGAGTCAGTAACATTTACATTATAGATTTACTATAATTATTAAGTAAGGGAACAAATACAAAAGCGCATACAACTTGTAACATTGACACATTTATGTTATTTGATGTGGTAAGAAAATAAAATTGAATATAAATTGTCTCTTAACAATTGGGTGAAGAAGTGGCTAGAACAGTATTTTTGACTTTCACCTTATCTTTATTATTGCTTCCCCACCAGAAAAAATATGTAATTAATTAAATCTAATTTATCCCCAAGGAGAGAACTTAATGCTAAAAAAGATGTTGTCAGGTAGGATTGATTTTTGGAGACCCACAAACCACTGTAATATCTAATATATTTTCACACCTTTCACACCTACCCCCATCATCATGACTAATTTACTTCTCCCTTCTTTAGGATTTCCCTTGTGGCTCAGACAATAAAGTGTCTGCCTACAATGCAGGAGACCCGGGTTCAATCCTTGGGTTGGGAAGATCTCCTGGAGAAGGAAATTGCAACCCACTCCAGTATTCTTGCCTGGAAAATCCCATGGATGAAGGAGCCTGGTAGGCTACTGTCCATGGGGTTGCAAAGAGTTGGACACAACTGAGCTATTTCACTTTTCACTTTCTTTAGGGAAAGATATTTCCCTGTTGACAAAGCATGACCTAAATGCTGATATTTGGCATTTAATGTGCCTGACCGAAGCATCTTGTAGAAGTCTGTCCAAGCCAGTGAAGGAGACTGATGTGTGAACACTGGGAAGTTTAAGTGGGCCTCAGAAATCAACTACAATCAATAATGCAAATCATTCATGATGCAGATCATTGAGAGCTGACGATGCATGGATCCTAGAAGTCCTACCCTTCTCTATTTACAGTGTATGACTGCTAACCCTTAGATTTATATATTACAGATTACCAGAATGACAGAGGTCATATCACTTAAACTTCCCACCATTGGGAATTGAGATGGTTTTCCTGAGTAGTTCAATTTTTACAAAGGACAGGAAATTTCCTGAAGATAATTGAAAAGGAGCAATGAAGGGAAATCTAAACTTATCAGCTTCTTACCTTCCATATTATTCCTAGATTTGGACCTGGTACCCCAGATAACTGCTTCTCTTCTTTGTCTTTTTCCAG
Seq C2 exon
AGGAAGCAAAAGGAAATCCAGGCAAAGAAGCATCAACTGACCAAGATTGAGGACCTGGGAGAAAGCTTAGAAGAGGCTCTGGTCCTGGACCTTAAATATAGCACCATCGGGCTGGCTCAACAGTGGGACCAGCTCTACCAGCTTGGGATGCGAAGGCAACACAGTCTAGAAGAACAAATCCAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.048
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(16.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(55.9=90.5),PF134991=EF-hand_7=PU(9.0=12.7)
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:
TCTTTGCTGAAAGAAACAGGAACAC
R:
TGGCTTGGATTTGTTCTTCTAGACT
Band lengths:
238-1591
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]