DreINT0023558 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6178350-6179997:+
Coord C1 exon
chr14:6178350-6178665
Coord A exon
chr14:6178666-6179822
Coord C2 exon
chr14:6179823-6179997
Length
1157 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGA
5' ss Score
7.83
3' ss Seq
TGTTGTTGTTGTTTTTAAAGCTG
3' ss Score
7.61
Exon sequences
Seq C1 exon
AGCTTACTGTCTCCGGTGGCGTTTGGCTTTGGCTGTGAGTATTTTGCCTTGTTTGAGGAGCAGGGTGTGGGTATTCAGTGGAATAACCTCTTCTCCAGTCCCGTGGAAGAGGACGATTACAACCTCACCACCTGCCTCATCCTCATGTACTTTGATGCCTTCCTGTATGGGGTCATGACCTGGTACATAGAAACGGTGTTCCCAGGACAGTATGGCATTCCCAGGCCATGGTACTTCCCTTTCACTAAATCCTACTGGTTTGGAGAGAACAGCACAAACAATACTGCAATACACGGAAAGAAGAGCAATGCAGGGG
Seq A exon
GTAAGACATCATTGTGATTCCACCTTTTATTTATATATATCATCCCACATAGCAAAATTTCTCTGGCCCACAGTCAGCTTTTGCTTGGCCCACATGCTGCAGCAAATTATTCAATTCAATACAATTAATCTTTATTACTGTAGCGCTTTTACAATGTAGATTGTGTCAAAACAGCTTAACATGGTAGTTTTAGTAAATTGAAACTGTGTCAGTCCAGTTTTCAGAGTTTGGTTTAGTTCAGTTCAGTGTAGTCTAATTTTCACCTACAATTTTCACAAGCCAGTGACGAAAGTGAAGGAAAGAAACTTTGAGAGAAACCAGGCTCAGTGGCGCATGACCATTTCTTCTCTGGCCAAACTTCTTGTGCAGAGCTGCAGTCTAGGCACCAGAGGCTAAAGAACGCTGGATGGCCATTATGGAGAAGCTGCAGGTTTGTGTAGGTCACCGGCGGGTGTACAGGGGATCAATGCGGAGACTCATCTGTTGCTAGGATCTTTCAGAAATCAGTATCATGCTCTCCACTCCTCCACGACAACCATAGCATTTGCCCAGGATATGGCTAGGTCCAGGATTATGGAGACCCCTAGAAGTCCTCTATGGTTGGGATTATGTTAGTTGACTAGACAAAGTCTGGCTTCCAGACAAAGGGCAAACCTGGACCATATCCGGGCTCAGCCAAGTCTCAGCCAAGTTAATAACTGAGCCTGAACTGGGCTAGATATGTTGGTGTGTAGCGACTGCAATGAAATTGCTAGAACCGTGAAGTCTTGTGCTTTAGGCAGGCATGGGTGTGTTTTTTCTTGAAGCGACCTGATTGGTAGAATTTTTCACTTTATTCAAAAATAATTTTAATGTATTTTAATGAGTCAAGATAGGCCAAACTCATGCGGCCCACATATCAATTTTTAACATCTGGGACAAATACTACATTTCACATCTGGCCCAAGTCTTGTGTGTTGCCATAAAGATAGTGCCACCACTGCCCTACCCGGGCCATGTTTGGCCCACATCCTGTATGCCTGCTCTGCCAGCTTTATGCCAAATCTGGGCCAGAATTCTTTGCTACCTGGGATTAAATGCCAAATGTGAAAGACATAAGTTTAATTGAAAAGGGCAAAAATTAAATCTGTCTTGTGTTGTTGTTGTTGTTTTTAAAG
Seq C2 exon
CTGTTTGCATTGAAGAGGAACCTACTCACCTTAAACTGGGAGTTTACATTGAGAATCTGGTGAAGGTCTATCGCCATGGTAAAAAGCTAGCCGTGGATGGGTTGACACTTGGTTTTCATGAAGGTCAGATAACATCCTTCCTGGGTCACAACGGAGCTGGCAAAACCACCACCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:17
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=PD(18.5=57.5)
A:
NA
C2:
PF0000522=ABC_tran=PU(18.6=45.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGGGTGTGGGTATTCAGTG
R:
CCCATCCACGGCTAGCTTTTT
Band lengths:
358-1515
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]