BtaINT0140387 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000888 | SPTA1
Description
Bos taurus spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206588]
Coordinates
chr3:11174953-11177141:+
Coord C1 exon
chr3:11174953-11175150
Coord A exon
chr3:11175151-11176997
Coord C2 exon
chr3:11176998-11177141
Length
1847 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TTTAATTTTAACCCCCATAGTTG
3' ss Score
5.88
Exon sequences
Seq C1 exon
GAGCATCGTGCTGACATGGAGGCCCAGGCTCCCGCCTTCCAGGCCTTTGAAGATTTTGGTACAGATCTTACAATCAGTGGGCACCGGGCCAGCCCCGAAATTGAAGAAAAGCTTCAAGCTGTTAGACTAGAGAGAGATGAGTTGGAGAGTGCTTGGGAACAACGCAAAAAGATGCTAGATCAGTGTCTGGAGTTGCAG
Seq A exon
GTACTGCAAATTCCCAATCGTTAAACAGGCTTAGCTGAGTCTGTTCCTTCTACGCAGTTTCACAGAGTTAATACAGGTGCTTATTTCACTGGAATTCCATTCCAAAATCATAAAGGTATCTCTTGATTATCTGACATTGCATTTTCTGCTTTGCATTTTCTGATCATTGTAGTGTTCTTTGCTCCTATTCTTGTTAATGAAAAGCTAAACAAAATGGAGGTCAGTCCTAGGGCATGGGGCCCTGAAATTAAGTGGTTATAATTTATTGATATTTAAACTTACTTATTGATTGAAAGTTTTACTGATTGATTTTTATTGATTTTATTGTGTTCCTAGAAACACATATCAGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGGTGGAGGAGCCTGGTAGGCTGCAGTCCACGGGGTCGCTAGGAGTCTGACACAACTGAGCAACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATAGCAACCCACTCCAGTGTTCTTGCCTGGAGAACCCCAGGGACAGGGGAGCCTGGTGGGCTCCGTCTCTGGGGTCACACAGAGTCGTACACAACTGAAGTGACTTAGCAGCAGCAGCAGGAACACAAATATTAGTAAGATAGTGTCTATTTTCTAAAAGTAGTGAAATTAGACTTGTAGACAGATCATTGGAAAAGACCCTGATGCTGGGAGGGGTTGGGGGCAGGAGGAGAAGGGGATGACAGAGGATGAGATGGCTGGATGGCATCACCAACTCGATGCACATGAGTCTGACTGAACTCCGGGAGTTGGTGATGGACAGGGAGGCGTGGAGTGCTGTGATTCATGGAGTCGCAAAGAGTCGGACATGACTAAGCAACTGAACTGAACTGAACTGAACTGAGGCAAATCATTCTAATATATAAAATAATTACTGATAAAATGTGTGAATGTTTTGAGATTATAGCAGAAGGAGTGATTAATGGTCCTGAGGGAAGTGAGTGAAAATGTCACATGCTGTTCTGAAAAGCAGTCTTTGCCAGAGTCTTAAAGAAATAACCAGCCAGTTTTCACCAAGTGTGTGTGTGTGCGTGTGTGCGTGTGTGTGTGCATGCTCAGTAGCTCAGAGTGTCCAACTCTTTTGTGACCCCATGGACTGTAGCCCATGGGCTCCTCTGTCCATGGAATTGTCCAGGCAAGCATACTGGAGCAGGTTGCCATTTCCTACTCCAGGGGATCTTCTTGACCAAGGGATCAAACCCACATCTTTTGCATCTCCTGCATTGGCAGGTGGATACTTTACTACTGTGCCACATGGAAGCCCGTTTACCATGTCTAGGATATGGAAAATAGTACTGCAAGAATGGAGGAAAGCTTATATGAAAACATAAAACATGTTTTCAGGGAAGAGTAAAAGGTCCAAGATAGCCAAGGTTTATTGTGTGAATGTTTCTTGAAAGAATATTGACATCCTTTCAGATCAGTTCAGATCAGATCAGTTGCTCAGTCATGTCTGACTCTTTGCAACCCCATGAACCGCAGCACGCCAGGCCTCCCTGTCCATCACCAACTCCCGGAGTTCACTCAGACTCATGTCCATCGAGTCAGTGATGCCATCCAGCCATCTCATCCTCTGTTGTCCCCTTCTCCTCTTGCCCCTAATCCCTCCCAGCATCAGAGTCTTTTCCAAGAGTCAACTCTTCTCATGAGGTAGCCAAAGTACTGGAGTTTCAGCTTTAGCATCCTTTACAGGGTCCCTATTATCAGTATCATGGGAGAGGTGGGAGATCATTTCCTCTGTCTGCCTGGAATGAACATACCATATACATTTAATTTTAACCCCCATAG
Seq C2 exon
TTGTTCCGAGGGAACTGTGATCAGGCTGAGAGCTGGATGGTGGCACGTGAGAATGATCTAAGGTCGGATGATAAGGGGTCCTTAGACACTCTGGAGGCCTTGATGAAGAAACGTGACGATTTGGACAAAGCGATTACTGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000888:ENSBTAT00000061417:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.258 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.2=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:
CATCGTGCTGACATGGAGGC
R:
TGGTCAGTAATCGCTTTGTCCA
Band lengths:
338-2185
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]