DreINT0023580 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6193932-6195528:+
Coord C1 exon
chr14:6193932-6194055
Coord A exon
chr14:6194056-6195398
Coord C2 exon
chr14:6195399-6195528
Length
1343 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TCTTTCTTACCTTACATAAGGTG
3' ss Score
4.52
Exon sequences
Seq C1 exon
GAAATTGGAGGAATTAATGACATCCTGAAGAACGTTTTGCTCATCTTCCCACATTTCTGCCTGGGTCGAGGTCTCATCGACATGGTGAAGAATCAGGCCATGGCTGACGCTCTGGAGAGATTTG
Seq A exon
GTAAGAATAGCTTGCTCTGACTTATATGCAAGTTTTCAGGATGTTGGAATTAAAATGATTAAGCACAATAAAAATGTTTTTCTTTATGAATTTTATATTAAAACCAACACAGTTCATTTACTAAGGACTTACTGCCTTTGCTATTAACATAGCTTTTGCAAGTTAAAATAGTTTGGTCAAAACTTAAAATTCACATGCCATTTGCTTACCCTCAAGATGGTCTAAACCTTTATGAGATTTTTTTTTTATTCTGTTGGATACAAAAGAAGATATTTTGAAGAAAGCTGAAACTATAGCAGGACAAAACAAATACTATGAAAGTAAATAGTTACAGGTTTTCAGCATTCTTCAAAATATCTTCTTTGGTGTTCAACAGATAAAAGAAAGTCAAACAGTTTTGGGTCAAGTGAAGGATGTGTAAAAATCATATAACCTCACTATACAAAAAAAGATGGATGTATTAGAAGGTTATTATAAAAATAGCAATTTCTACTGACAATAACCGAAAATAAAGAACATCAAAATTAATTCTCTGATTTATAATTATAATTTTTTTTTGCAAATGACTGTGTATTTGACAACTTCTGAAAAAGCTAAGGAAATAAACTCAAAATGGACTCTTTCCTTATATTTTCTTATCGAAATTGTGAGACATAAGCATAGAATTGTGGGTTCATTATCTTTAACTCCAAATTGAAGCTTCATTCATTCATTCTTTTTGGCTTAGTTTCTCCATTACTGGGAAACATCCATACTCATTCACACACATACACTATGGACAATTTTAGTTTACCCTATTCACCTGTTCCCCATGTCTGTGGACTGTGGGGGAAACCGGAGCACCCAGAGGTAACTCCACATAGAAACGCCAACTGATCCAGCCAAGGGTCGAACCGGCGACCTTCTTGCTGTGAGGCGAATGTCCTACCCACTGTGCCACCATGCTGCCCTCAAATTGAAGCTTTTTACACAATTCTAGAATTCATTTTCTGAGAATTCTTTCAGAAGTTGCTAGATGGAAAGCTGCATTTGTGAGGAAAAAAACGCCAGAAATGTGACAAAGTTTTCTTTTTTTACTTTGGCTTAAACAGGCTTCCATAAATTTCTTATAATTATCATGAATAAGTATTTCATTTAACTTAACTTATTACCTTGTTAGGTTTCCAGTTCCAGTTATTTATAGGAATGCAGGCATCATTCTTCAATTTAAATAATTCCGATATGTGAAGACTAAATATTATCGTTTAATCCTTTAAAAGTGCATTGTCCGCTGTATTTTGAAGTAATTAATTACTACTGAGGCATATGTATTAGATGCTGAATTCTTTCTTACCTTACATAAG
Seq C2 exon
GTGAGAACCGTTTCCGTTCTCCACTGGAGTGGGACATGGTGGGTAAGAATCTTTTCGCTATGGCTGTGGAGGGTGTGGTTTTCTTCATTATCACCGTCCTCATCCAGTACAGATTCTTCTTTGAACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:37
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=FE(12.6=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PD(10.2=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAATTGGAGGAATTAATGACATCCT
R:
TTGGGTTCAAAGAAGAATCTGTACTG
Band lengths:
254-1597
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]