BtaINT0010799 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020661 | ABCA1
Description
Bos taurus ATP-binding cassette, sub-family A (ABC1), member 1 (ABCA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001024693]
Coordinates
chr8:96312610-96314044:-
Coord C1 exon
chr8:96313840-96314044
Coord A exon
chr8:96312724-96313839
Coord C2 exon
chr8:96312610-96312723
Length
1116 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
CATCTGTGCTTGGATTTTAGGCC
3' ss Score
8.36
Exon sequences
Seq C1 exon
AGCCTGATGTCTCCTGTGGCTTTTGGGTTCGGCTGTGAGTACTTCGCCCTTTTCGAGGAGCAGGGCATTGGGGTACAGTGGGACAACCTCTTTGAGAGCCCCACAGAGGAAGATGGCTTCAACCTCACCACCTCCGTCTCCATGATGCTGTTTGACACCTTTCTCTATGGGGTGATGACGTGGTACATTGAGGCTGTGTTTCCAG
Seq A exon
GTACACTGGACTTCCACACTGCTTTTGTCTTCATCCAGGAAAAAGAAATTTCTAACCGTGTCATTTTCCTCACTTTGTGCTGGAATTTCTGCAGGGCCCGGGTCTCCTTGGAAAGTGGTTAGGGCTTTAGACCTATGGCAAACAAATTATCTCTAAGAAGAAGCTACTGATGCTAAAAGTACAGCTTTTACTACTGACCTAACTCTTATTTCTTGAGCACTGTGTGCCAGGCACCTGATGCTTTGGTTCAATTTAATACTCATAAGACTGCTGGGAGGGAGTTGCTGTTCTACCCAGTTTTTGCAAATGAGAGAAGTATGATGCAAAGAAGTTAAATAACTTACCTGTGGCCACATAACTGGTAAGAGTAGGTGCTGGGAGGTGAACCCAAGTGAGTTACACTGAGTCAGCTTGCCCAGCAGAGTCCTCTCAAGCTGAACCAGGTCTCGAATTCTGTTTCCCCTGAGTTACCACCAGCAGAGGTTCTGTTTCCTGAGTACAGCTTGTGAATAACAAGATACATATTGGTGCTAAGCCCTTGCCTGTGTTTTAATCAAAAGTCATAAAAGTTCATTTTTATACTTCCATAATAAGTCTTCTTGACTGAGACCTCCCTTGGATATATTTTCATAGAAGATCAAATTCTGAGAGAGCGAGGTTTAACCCTTTCTGGTTCACTTTCTGATTTTTCTCCAAAGGAGTGGCCATGGAATATTGATTACCCATCCCTACTTGGACTACTTGAATGTCCCACACTGAATGTGCAATTTTGTATTGTACAGATCCGGATTCAGATTCTGAGTCCTTCACTTCACTGGCTGAGTGATCTTGAGTGGGCCACTAATCCCTCAGTCTCCTCATCTCTAAAGTGGGAATGATAACCTGCCTCATGGGGTTGCTGGCAAGATTCAGAGAAGTGCAGGGTGTTTGTCATACATAGTAGAGTTCAGCAAATGTTAGCCCCTCCTCCCCCACCTCCATTCCATTCTGTCCTGTCTCCCAACAGCTGTGTCAGGGGGAGACATCAAGGAAGCTGTGTCTGGGATACCTGGCTGGGATACCTGGGGGTTGCTGGGGCATTACAGAATTTGGCTCACATCTGTGCTTGGATTTTAG
Seq C2 exon
GCCAGTATGGAATCCCCAGGCCCTGGTATTTCCCTTGCACTAAGTCCTACTGGTTTGGCGAGGAAAGTGATGAGAAGAGCCACCCTGGTTCCAGCCACAAGGGAGCATCAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:17
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=0.308
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(24.5=88.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGATGTCTCCTGTGGCTT
R:
TTTCTGATGCTCCCTTGTGGC
Band lengths:
318-1434
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]