BtaINT0011254 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006896 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:HGNC:39]
Coordinates
chr19:62111410-62113250:+
Coord C1 exon
chr19:62111410-62111595
Coord A exon
chr19:62111596-62113102
Coord C2 exon
chr19:62113103-62113250
Length
1507 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ATCTTTTTTTTTTTTTCCAGCTT
3' ss Score
9.93
Exon sequences
Seq C1 exon
ATAACGTTAGCTTTCCTGATGAGCGTGTTAGTGAAGAAACCCTTCCTTACGGGGCTGGTGGTCTTCCTCCTCACTGTCTTCTGGGGGAGCCTGGGATTCACAGCTTTGTACAGACGCCTTCCTGCGGCTTTGGAGTGGACCTTATGTCTTCTTAGCCCCTTTGCTTTCACTGCTGGAATGGCCCAG
Seq A exon
GTAAGAGTTCATGAGACTATTTCACTATTTCACTCACTGTGTGTGTTAATCGCTCAGTCGTGTCCAGCTCCTCTGTCCGTGAATTCTCCAGGCCAGAATACTGGAGTGGGGAGCCGTTCCCTTCTCCAGGGGATCTTCCCAACCCAGGGATTAAAGCCAGGTCTCCCGCAATGCAGGTGGATTCTTTACAGTCTGAGCCACCAGGGAAGGGACTAAGCACAAGCTATGATGTTGTAACTAGAATTACATTTTCTGAGAGGAGGTCAGTCTCGTATAGAACTGGCCAATCAAGAAACAAAAATGTGCTCTAGGATATTGCTGGTGGTCCAGTGGTTAAGAATCCGCCTGCCAATGCAGGGGACACGGGTTCGATCCCTAGTCTGGGAAGCTTCCACATGCCGCAGAGCGACTAAGCCCGGGAACCGCAACTGCTGAGCCTGTGCTCCAGAGCCAGCGCTCAGCAACGTGGGAGCCACTGCAGTGAGAGGCCCCTGCGCGGCGGTGAGGAGTAGACCCTGCTCTTGCCTCGACTAGAAAAAGCCTGCCACAGCAATGAAGACCCGGCACAGCCACAAATACATAAATAAGTGAATCTTAACAATGTCTCTAGGGAGTTACTGGTTTTCAAATACTGCTGATAACATGAAGGGTCATGTTTCCTGAGCATTAAATGAAATAAACGTTCTTTGGGGGACAGCCCTATAAAAGTAAAAGCTGACCACACCATCAATGGGGTGTCAGTCTATATTAATCAGATCTAAAAGAAAACGGGTAATGCTGAGAGAGAGAAAGAAAAACCTTTCCTGTCTTTTCAATCTGCACCTTCACAAAAGCAAATGGGAATTTTAACCTTTAGTATGTCGCGTGAGTTATCCAGGGGGGATCTAAAAACCTTCCCAGGTGGCACAGTGATAACAGAATCAGTCTGTACTGCAGGAGACACAAGAGACATGGGTTTGATTCCTGGTTAGGGAAGATCCCCTGGAGTAGGAAATGGCAACCCACTCTAGTATTCTTGCCAGGAAAATTCCATGGACAGAGGAGCCTGGCGTGCTACAGTCCATGGGGTCACAAACACCTCTACTAAGAAATTATTCTTCTGTCTTCTGCCTGACTGCAAAAGTACTTCAGCCCTCTCCCTTTCAGTCTCAAATAGCGTCCCCCCTCTAGAACTACCCCCTCTCCTCCACAGTCAGCCTGATGAAGCCCCCAGGCAGCCTAGCTCCAGTATCAGCTTCCTGGTTTTCACCTCTGCCTGGAGGACTTCCCTGTTGCAGAGTGTGGCCTTCTAAATCCTGAGCACCACCTTCACTCACTCCCTGAATTGCTTTGTGGTTAGATGGTTTCCTTCCTGTATCTTCCAACAGATTAGTGCTCTATGAAGACAGAATCATGTTTCATTTATCTTTTCAATTCCAATGTCTAGCAGAAATAAGACAATAATAACTTTTAATGCTCTAGGTATCCTTTTTCAATTCCACACATGTATCTTTTTTTTTTTTTCCAG
Seq C2 exon
CTTATCCATTTGGACTACGACGTGAATTCTAACATCCATTCAGATTCTCCAAACGACCAGTACCTCATAATAGCTACTATTTTCATGCTGGTTTTTGATGCTCTTCTCTATTTGGTATTGACGTTGTATTTGGACAAAATTTTGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006896:ENSBTAT00000009067:8
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:
PF126982=ABC2_membrane_3=FE(15.6=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PD(10.7=84.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTTAGCTTTCCTGATGAGCGT
R:
GGCAAAATTTTGTCCAAATACAACGT
Band lengths:
328-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development