BtaINT0010805 @ 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
chr8:96307477-96309082:-
Coord C1 exon
chr8:96308945-96309082
Coord A exon
chr8:96307698-96308944
Coord C2 exon
chr8:96307477-96307697
Length
1247 bp
Sequences
Splice sites
5' ss Seq
AAGGTCACT
5' ss Score
3.39
3' ss Seq
CCTGTGTTTGTGCCTGGCAGGCC
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTGGAATGCAGAGAAAGCTGTCTGTGGCCTTGGCCTTTGTTGGGGGATCCAAGGTTGTCATTCTGGATGAGCCCACAGCCGGTGTGGACCCTTACTCCCGCAGGGGGATATGGGAGCTGCTGCTGAAGTACCGACAAG
Seq A exon
GTCACTGACGTGTATTTACTCTGTCTTCTGGGCTGGGAGCGGGGAGAAAGGGGGAGGGAGGGGCTTTCAAAGACTGGCTGTATCTCAGGGCTGTTCCTGCTAGAGTACCAGAATTGCTTCTCAAGGAGAATATGAAGCTGAACTATGAGATCAGCCCTGGTCTGCAAGTAGGAGGCCTGGTTTACAAGACACTTCAAGTTTCACTTCAATCCCTAGGGGCCTGCATGGGGGAGGGAAATGGGGACAAGGGACGTCCTCTGTGGGGCCCCTGGGCCCCCTCCAACATAGAACTTTCACTTGCCTAGTACAATCATGGTCCCCCGCAGACAGATTCCTGAGAGCCGAGACTGTGTCGACCTATATCTCTGTCCCCACGTGGTGCACTACGCTTGCATGTTGACAAAGTAGAGGAACACTTGAGTGGATGGGAGAGTTGCAGTCAGTTTGTGTGACCCCATGGATTGTAACCTGCCAGGCTCCTCTATCTGTGGGATTCTCCAGGCAAGAATACTGGAGTGGGCTGCCATGCACTCCTCCAACGGATCTTTCCGACCCAGGGCTTAAATCCGCGTCTCCCTGGGGCTCCTGCATTGCAGGTGGATTCTTTACCGCTGAGCCACCAGGGTGGAAGATACATAGGATGGTGTGGTACAAGGGGCACAGGTTTGGAGTCAGCTCAAGTTGGCCCAAGACTTTGGAAAAGCCATTAAACTTGCCTCAGTGTCTTTATCTATAATGGTGGTTAATTCCTACCTTATGAAAAGTGGAAGTCGCTCAGTTGTGTCTGACTCTTTGCGACCCCATGGACTGTAGCCTGCCAGGCTCCTCTGTCCATAGAATTCTCCAGGCAAGGATACAGGAGTGGGTGGCTATTCCCTTCTCCAGGGGATCTTCCCAACCCAGGGATTGAACCCAGGTCTACCACATTGCAGGTGGAATCTTTACCAACTGAGCCACCAGGGAATCCCATCTTATGAACGATTTAGTTAAATGAGGCCTAGCATGTAGACCACCTAGCACACTGCTAGCCTGAAGCTAGTTCCCAGATAAACATTCCCGCCCTTTGTTCTATGAGGATGCAGAGCTGTCCTCAGGACATTACCCGCCTGGGGGTCACAAGCACACAGCCTTGGAGTATTTCTCCCAGGCGTGGCCCCGCCGGCTCTTATTTCTGTAGCTTCGGCCCCTGTGAGCAGTGAAGATGGCCAGCCTCACCTGTGCTATGTCCCTGTGTTTGTGCCTGGCAG
Seq C2 exon
GCCGCACCATTATCCTCTCCACACACCACATGGACGAGGCAGACATCCTGGGGGACAGGATCGCCATCATTTCCCATGGGAAGCTCTGCTGCGTGGGCTCCTCCCTGTTCCTGAAGAACCAGCTGGGGACAGGCTACTACCTGACCCTGGTCAAGAAGGACGTGGAGTCTTCCCTCAGCTCATGCAGAAATAGCAGTAGCACTGTGTCATACCTGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:22
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:
PF0000522=ABC_tran=PD(17.8=55.3)
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:
AGAAAGCTGTCTGTGGCCTTG
R:
TCAGGTATGACACAGTGCTACT
Band lengths:
343-1590
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]