BtaINT0010812 @ 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
chr8:96298710-96300482:-
Coord C1 exon
chr8:96300358-96300482
Coord A exon
chr8:96298809-96300357
Coord C2 exon
chr8:96298710-96298808
Length
1549 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
TGCCTCTCATGTATCTACAGTAA
3' ss Score
6.88
Exon sequences
Seq C1 exon
ATTGTCCTGCCAGCTGTGTTTGTCTGCATCGCCCTGGTGTTCAGCTTGATTGTGCCACCCTTTGGCAAGTACCCCAGCCTGGAGCTTCAGCCCTGGATGTACAATGAACAGTACACATTTGTCAG
Seq A exon
GTATGCACTTGCCTTCTGCCTCCAGGGGGAGAGGAGGGCTCAGGCTGACCAGAGTGTTTACTATACTGAGGGCCAAGGGGAGGGGGACTCGGTTACACAAGGGCACGGATTGATCAGCTGTGGCTGCAGCCCTCACACAAGCTCATGCTAGATGCGAGAACAGCAGTGAACCAAACCTGAAGTAGCAGGGCTTTGAACTCATTTCCTCTCTATTCGTTGTTGTCAGGAACATACATGCCTTATGTAAATAATCTGCCAATGCAGAAGAATCTTCTTGAACTATAATATACTTGGATTTTTATACTAAGTCTTTATTTTGCAGTTGAACACAGGGTTTCCATACACTCAGACCCTCACACCTCCAAGTTCTTGTTTTCTACATAGTGCAATTCACATATTTATTATTTCATCTTTGCTAAGTCGCTTCAGTCGTGTCCGACTCTGTGCAACCCCATACAGGGCAGCCCACATATTTATTATTTCATCTTTGCTAAGTCGCTTCAGTCGTGTCTGACTCTGTGCAACCCCATAGACGGCAGCCCGCCAGGCTCCCCCATCCCTGGGATCCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGGGAAGTCGCTCAGTCGTGTCTGACTCTTCGCGACCCCATGGCCTGCAGCCTACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTATTTCATCTTTAGGTTACATATAATAGCTCCTGTTTTTTTAGACAAAAATACAGCTATCCTGTGACAATCCAGTGCTTCAAACAAAAGAACAAAGGAATTTCTCCATCTCCTTATGCAGGAGTTTTCCTCAGTCCCACAGTATTTGCAAACCTTTCTATGGATAAGTGTGCCAGTGATGTCCAAGGGAAGCTTCAGGGAAGCTTTAAAAAGAAAAAGGAAACATAAGCATGCAAATCAGCTTCCTGTTCTCTGATTCTGTGCTTTCTTCCTATTTTGTGCGGGTTTACCTCCTTCTTTTCTTTCCCAGCTGCTGACCTTGTGTTGCCCAGGGCTGTGGAGCATGGGCTTGTTTTGTGTTTATAACTTCTGCCCATCATTATTTGTGCTTTCCAGTTGTCCACGCAAATGTTAAGCCCATAAAATCTGCCTTCCTTTTCCTAGAAAACCCCTCTTGTCTATGCCTAATGATTAATTGTGAAAGTACTTTTGAAATACTGATCTTTAATGAATTCATGTACTTCCCACTAAAATAGATATATGTAAATGTATGTGGGTGCACGTGTACGCACCCCTCCATATTTATCACTTATTTACACAAGTTCCACTTTGGAGTGCTGTATGTTATCTTGACACCAAATAAACAACCAGAGGCTGAGTTACTTGTGGGTGGGTTCTGTGTTTCTATTTTAAGAGCTTGGCAGGATTTGGCACACAGGAAGTACTTAATAAAGTGTTAAATTTGAAAAAAAAAAAAAAGTGCCTTTTCTTCTCCCATTCATGGTTTAAATGCGTTGCTAAGCTGACTGCCTCTCATGTATCTACAG
Seq C2 exon
TAATGATGCGCCTGAGGATGTGAGCACCCAGGAACTCTTAAACGCTCTCACCGGAAAGCCTGGCTTTGGGACCCGATGTATGGAAGGAAACCCGATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:29
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=0.088
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(7.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(6.3=100)
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:
ATTGTCCTGCCAGCTGTGTTT
R:
GGGATCGGGTTTCCTTCCATAC
Band lengths:
224-1773
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]