BtaINT0010796 @ 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
chr8:96317414-96319343:-
Coord C1 exon
chr8:96319167-96319343
Coord A exon
chr8:96317637-96319166
Coord C2 exon
chr8:96317414-96317636
Length
1530 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
ATCCTCCCCTACCCTTCCAGCTT
3' ss Score
8.49
Exon sequences
Seq C1 exon
GTACTGGGACCCTGGTCCTCGGGCTGACCCCTTTGAAGATATGCGGTATGTCTGGGGAGGCTTCGCTTACTTGCAGGATGTGGTGGAGCAGGCAATCATCAGGGTGCTGACGGGCACAGAGAAGAAAACTGGCGTGTACATGCAGCAGATGCCTTACCCCTGTTATGTTGATGACAT
Seq A exon
GTGAGTTACCAGTAAGCTGCCACCTTTACTTAACTGGTTAGCACTGTCCGCAGGTGGGGTGTGTATACACACACACACACACGCCAAGAGAGGAAACAGAATGCTTTGGTTAAATTTATTTTATATGTGTGTTGATACTGGTCAAAAAATTGATGAAAACAAGACTATGGCTACTGCAAAGCAGCTGTTTTTGAAGTTGTGTGGAGATTTCAGGAAATAAGATGCTAGATGTAGGTAGTTGACAGTTTGAGGCACAGGCACACATGAACACACACCACACACCAGTAATCCTCACTCCTTTCTGGTCTATGGTTACTAGAACTTTTATTTTTCATACCCTATCCTTTTGGTCAAAATTGGCCCAATCTCCAAGTTTAAAATGTGTCAGGACGAGCACATGCCAAATATATTCACACATCCATACGTCCCCCAAATACAGAGGCGCGGTGTTATGGACCTTGAAAAGCTAACTTCACATCAGTTTTTCTTCTTCTCTCAGAAAGTGGTAAGCCACATTTTCAAACAATGCAAATAAAACTGAACAAGTCCATTTTATCTTAGACTTTTTAGATAACCTTTGAGTGCTTAGTCACTGTGCTACCAAGTGGGGTCTGTGGCTCTATGGCTCATGATTTCTTGTGAGAGCAAGAATGGGGCAGAGGTGTAGTTATTGCAGGCATCTGAAGTATGTCATGTCTCTTCCAAATTCTGGAAACTCTTTCATTCTCTGTTGTGTGAGGGTGAGAGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATAGAGATCAGAGTGCAGAAGTAGCAGGGTTACTCTCCTTGTATCTCTCCCAGCTTCTTATTGAACCACACTTTTACTTGCAGGGTTCATTCTAGCTGTTCGGTTCACCTGGATTTATCTTGTTTTTCACCTTCAGAAAGACTAGCCAGTATTTTCCAATGACGCCCCTAAGCAAAGCTTTACTCTAGAAAGGACATATTAAGATGGGGACACGCCTGTTGTCACATACCCTGTAAGTGCCTAAGTGGTAAAGCTGAGACTTGAACCTTGAGTTTTAGAGTCTAGATTCTGTATCCCTTTGACTTCGCTGCATTTCATTTTCTAGTTTGGAATCTGAAATCTGAAATGTTACTGACAGGAGCTGCATAAAGTGTGTTTCTGCACCATCTGTCGTAACAGTTGTGCAAGGCAAGCTGATAGTGAGAAGACCTTGAAGATGTTGAACTTTCATGAGACAATGAGTTGGGTTTTTGGTTTTGTTGGCTTTGTTTTAGTACTTTAAAACCACATTTAGTTTAATGACCTCTGATAGTTATCTAGCTACTAAAGCAAGCCCTCAAAGAACTTTGGCATCACTTTGTTAATAGTTTGTAATCACTGCATTGCCCCGCTCACGAAGCATTCCTGTCAGGGTGCACAGGTCTGCCCATCTCGGGCTTGGTCCTGGTGATTCCTCTTGCATGCCAGCCCAGAGTTGTTGGCCCAGGAGCCTGGCTCACTCTTGCCTTTAATCCTCCCCTACCCTTCCAG
Seq C2 exon
CTTCCTGCGGGTCATGAGCCGGTCCATGCCTCTCTTCATGACGCTGGCCTGGATCTACTCGGTGGCTGTGATCATCAAGGGCATTGTGTACGAGAAGGAGGCACGGCTGAAAGAGACCATGCGCATCATGGGTCTGGACAACGGTATCCTCTGGTTCAGCTGGTTCATCAGCAGCCTCATCCCTCTGCTCGTGAGCGCCGGCCTACTGGTGGTCATCCTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020661:ENSBTAT00000027538:14
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:
PF126982=ABC2_membrane_3=PU(15.3=63.3)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(29.7=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:
GAGGCTTCGCTTACTTGCAGG
R:
TCAGGATGACCACCAGTAGGC
Band lengths:
342-1872
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]