BtaINT0011235 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006896 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:HGNC:39]
Coordinates
chr19:62134383-62136436:+
Coord C1 exon
chr19:62134383-62134490
Coord A exon
chr19:62134491-62136262
Coord C2 exon
chr19:62136263-62136436
Length
1772 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGA
5' ss Score
4.23
3' ss Seq
TTCTTTTGCTTCTTTATCAGAAA
3' ss Score
7.99
Exon sequences
Seq C1 exon
GAGCACACGTCTAACGAGCACGAGTACCTGGGCATGGCCTTCTTCTGGATCCCTGGGGCGGCCTGCTTCACTCCGTACATCGCCATGGGCAGCATCGGTGACCATAAA
Seq A exon
GTGAGAACAGCTATGCAGCCCGTGTCCTGCTCCGTACCCTGTAACACCCACACGGAGAGTGAGACGAAGTAGATACAGGCAGACGGACGACTGAATCACTCCGCCGTGTGCCTGAAACAACACGACGTTGTCAACTGACTATACTCCCATATGAAATAACAATTAATAAAAGCTGAGCAATAAGAAAAAATGCGACAAAAGGGATTAAGTCAAATTTCTCAAATTTTCCTCCCTGAGGGAAAAAAATGTTTCCTATACTAAGTAGTAATGATAGTAAAAAGCAAAAGTCCTTATATGTTCTTCTATATTTTTATTGGAGTATAATCGCTTTACCACGTTGTGTTGGCTTCTGTCTACAAGGTGATTCAGCCGCATGTACACACATATCCCCTCCTTCCTGAACCTCCCCTCCCCACGCCACCCCTCCCCCACCCCTCCCCGGGTCACCCCAGAGCCCCGAGTGAGCTCCCCGCGCTGTACAGCAAGCTCCCGCCAGCTCTCTGCCTCCCCACGCCACCCCTCCCCGCTCCCCCACCCGTCTCCCTTCCCATGCCACCCCTCCCCCCTCCCCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCGGGTCACCCCAGAGCCCCAAGCTGAGCTCCGGGCGCTGCGCAGCAGCTCCCACCAGCTTTCTGCCTTACACACGGTAGCGTATATGGGTCAGCGCTACTCTCCCAATTGCTATGTTCTTAACACCCTGTGACCCCGCCCCCGTCTTATGACCACACATGTATATGCGCATCGTGCACCTAATTTAAACAATGCTTGAAACAATGGAGGGTCAACCATTTGAATAAAAGCTTGGCGAATATACAGAATATGCTATTTGCCTTAAATGAGAGACCTCAGGAAGGATAGCTCAGAAGGTACCATCAACCGGCTGGGAACCTCGGATTCTGTCTGGCAGGTTCTACTTCCCTGCTGACACCATCCCATCCCCATTCCAGACGGAGGCGAGGTTCTCCGGTGTAACAGCCCTAAGCAAGGCACCAGAGTACTTTGGCTTATTGCTGGAAAAGAGTGTCCCTTTAAAGCTTCTTTTTGTGAAGATTCTATAAGAATGTCAGGAACCCACGGTAGACTTTCTGTGCATCCATGGTGCTTCCCTGCCACACAAGTTCCCTCCTCGTGTCTCCACGTCCTTAGCGTCCTCTGCTGGGGTTCCCTCTGCACCACTGAGCCTTGTGAAAGTTCAGCAGGTGCTGCTGGTGGACTCAAATTAATTTTCACTTACCCTGCTCTTAAACTATCCTTCTCTTGAGCAATTTCTCCCATAAGAAGCAAAGCAAGATGCCAGTTATAAGTGTGCTGTTTACATTCCGTGTAAAGCTTAAGAATCTTCCAGGAAATTGTGCACCTCCTTCTCTTGAAACTCTGTGCATCTTGCAAGGCAAGTGTCAGAGGCATCAGTAGCTTTGACAAGAAAAGAATAAGAATCTTCTCACCACGGCAATGCTGTGTAGATCCCTTCTTCCTGGAGACAAGGTGGCATACAGCATTATCAATGCCCCTGAAATAGGAACAGGGCAAGTCACAGTGTCACTTGCTAAATTAGCATAATATATAAGAGAGACAAAGGGGAAATGAATGCTTTTGTGCTGCATATTTGCAATTTCTCCAGCCTAAACTATTCAAAACTTTTGACGATTCTTTTGCTTCTTTATCAG
Seq C2 exon
AAAAAAGTTCACTCCCAGCTGCGGATTTCAGGCCTCTACCCTTCCGCTTACTGGTTTGGGCAGGCGCTGGTGGACGTTCCCCTGTACTTCTTGATCCTCCTTCTAATGCAAATAATGGATTATGTTTTTAACCCAGACGAGTTTGTGTTTATCATTCAAAACCTGGCAGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006896:ENSBTAT00000009067:23
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(12.2=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(19.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACACGTCTAACGAGCACGAG
R:
TGAACTGCCAGGTTTTGAATGA
Band lengths:
278-2050
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development