BtaINT0010810 @ 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
chr8:96302339-96303662:-
Coord C1 exon
chr8:96303549-96303662
Coord A exon
chr8:96302488-96303548
Coord C2 exon
chr8:96302339-96302487
Length
1061 bp
Sequences
Splice sites
5' ss Seq
CAGGTCCGT
5' ss Score
6.47
3' ss Seq
TTAGCGATGGCTTTTTGCAGAAT
3' ss Score
4.57
Exon sequences
Seq C1 exon
ATGGCACCTTACCAGCAAGACGAAACAGACGAGTCTTTGGGGACAAGCAGAGCTGTCTTCGCCCTTTTACTGAAGACGATGCTATGGATCCAAATGATTCTGACATAGATCCAG
Seq A exon
GTCCGTTTGGGCGAGATCTGTGTTTTGTTGCTTGAAAGTGAATTTCCCTCTTGTGTTCTCTGGTGTTATCTTTCAAGGCCCTTGAACCAGGATGATAGATGCCTACAGGGTCTAAAGAGAAGAGAGAGAATGAGAAAAGCCACTTTCCCCTTCTGGTGCTGTGCATATGATCAGACCTGAAAGAGCCTGTCCTCCCCACTTCCTGCACTGCACTGAGACCTCTCACTCGAGATACACATCAAAAGACAGCCCTTTATTCCTCTGAATCCATTTATTATCTTTTCCATAGAGTCCCAGTTTTCTCGCATTCATTAGGTGTTTAATTTTGGAATAAATGTTCTTTGAATGGGTGGATGATTTTGAAAGTGAGGTGAATTTGCTACTAGAGTTGATTGTACCCTTCAACTTAGCTGTTTTCGAAGACTGTATCCCTGTGTGTTTGGGATGGAGAAGGAGAGACAAGAAATCAAGCAAATATTGGTGAGACGTCAGGTCACCGCAGTGAGAAATCATTTGTATAAGTGAGGATTTCTATAAAACTGTTCTGAACAGAAACCTTCCTGGCTCTCCTGTCCAATGTGCAACTCTCGTGTTCTCTGTAACTTTATACATTGTTAGCACTTGGACCACCTGAATGTGTCCACCTTTTAGCCAGAGACACAATAGGCAGGAGACAAGTTGCTGTTATGTGTTCTCAAAGTATGTCAGCCTACAGACATGGCCTGTTTTACAGAATATTCTGTAAGAAATTGAGGATGACTCGATTCATTTGAATGGCTTGATGTAACTGTTATGTGTGCACACATCTCTTCAGTTGTCTCAAGGCACCTTCATTTTTCTGTGCTCATCAGACAAGAACCAAAGGCAGAGCCTGCTAGTGTGGTACATTTGGGGTCATACCTTTTCCATGGACGTCAATGTGTCATAAAAGCCCTTCATTCCTTTACTTCTACCTCCAAACACAAGCCTCCAAGGTGGTGGCTAACGATGCTGGAGGGAGGAGGCTGGGGATGTCAAAAATGCCTGGTATAATCGATGACCTTAGCGATGGCTTTTTGCAG
Seq C2 exon
AATCCAGAGAAACAGACCTGCTCAGTGGGATGGATGGTAAAGGTTCCTACCAGGTGAAGGGCTGGAAGCTCACACAGCAGCAGTTTGTGGCCCTTTTGTGGAAGAGACTGCTGATTGCCAGACGGAGTCGGAAAGGATTCTTTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.436 A=NA C2=0.140
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(1.1=12.0)
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:
ATGGCACCTTACCAGCAAGAC
R:
TGAGCAAAGAATCCTTTCCGACT
Band lengths:
262-1323
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]