BtaINT0010801 @ 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
chr8:96310310-96311915:-
Coord C1 exon
chr8:96311744-96311915
Coord A exon
chr8:96310442-96311743
Coord C2 exon
chr8:96310310-96310441
Length
1302 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGA
5' ss Score
5.58
3' ss Seq
CTTTCACATTTTTTCCTCAGGTC
3' ss Score
10.99
Exon sequences
Seq C1 exon
TCTGCATGGAGGAGGAACCCACCCATCTGAAACTGGGTGTGTCCATTCAGAACCTGATGAAGGTTTACCGGGATGGCATGAAGGTGGCTGTGGATGGCCTGGCCTTGAATTTCTACGAGGGGCAGATCACCTCCTTCCTGGGCCACAATGGAGCTGGCAAGACCACCACCAT
Seq A exon
GTAAGAAGAGGGTGTGGCTGGCTGAGAATCAGCCGCAGGAAGGGTCTTTCCTATAGTCAGAAACTCATACCTAAGGACTGCTGCTGCTACTGCTGCTAAGTCACTTCAGTCATGTCCGACTCTGTGCGACCCCATAGACGGCAGCCCACCAGTCTTCCCTGTCCCTGGGATTCTCCAGGCAGGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCGCTCAGTCATGTCCGACTCTTAGCGACCCCATGGACTGCAGCCCACCAGGCTCCTCTGTCCATGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATTGCCTTCTCCATGCCTAAGGACATTGTGTTGCTTACCCAGGCAAGGGCAGAGTGCATAAGGAGTTGATGAGTATAAAAATATCACCTAATCACGAGAATGTTTTCCAAATGCTGGATTTTCCTATCTTCGGGTTAAAATAGGCTGGGGACCTTTTGATGACCTTTCCCATTTGGTTCTCAAAATTCTGCAGTGTTTTAGAACCTGATGTTGTGACAGATCTGAGAAAGGGTTTCTTTGGGACTGGTTTGGTCAGGATTAGGAGGCAAGAATGTGAAAAGGAAGATAGGCTGTGTTGGAGAGATGAGGCAATTTCTGGAAACTCTGTCTCTAAGCAGATGTGAGGAACAGCTGGGCAGCTGGCTGTAAGACTACCTTCTCTGGGACCGATAAGAACCTTAATAATGAGCAGTTTCAGAAGGGAACATGGGCCATAAACATACCAGAGTTACCCTCAGTGGCTTTCAGTGTAGCCCATCAACCATTTCAGAGGGTATGTTGGTGGTGGGGGAGGTAACCTCTTTTTCCCGTTATGTATTTTTTAAATGCACAATTAATATATTGCAAAAATTGCAGAAAATCTTTAAAATCTAAAAAATCCTAACACACAAATTATTTTCGTCTTTAAATAATTGGTTTTACTTTGTCCATTTGACTTGAACATGATTTTAGGCATAAAAAATGTGTTTTAAAGTGTACTTCCCATTGCAAATTGGAATCTTTATTTAAAAAATGTGTGTGCTAAAATTGCCATTTCCAACACACAGGCCCACCCCTATCTGTTCACTGAGGCAAAGAGTCCTTTGCTGTGTGGGTGTCCCTTGGGGTCTCTTAGGAAGGAAAGAGGGTGGAGGGTTGCTGCCTCTGCTTTCCTCCAGGGCTCTGCAGCCTAGAATGGAGCGTCTCCAGGGCAGGAGGGCTAACGCTGACTCCTGTACTTTCACATTTTTTCCTCAG
Seq C2 exon
GTCCATCCTAACTGGGTTGTTCCCTCCTACCTCGGGCACTGCCTACATCCTAGGGAAAGACATACGCTCCGAGATGAGCACCATCCGGCAGAACCTGGGGGTCTGTCCCCAGCATAACGTGCTGTTTGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(18.5=46.6)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.1=100)
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:
TCTGCATGGAGGAGGAACCC
R:
CCAGGTTCTGCCGGATGGT
Band lengths:
270-1572
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]