DreINT0023587 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6202043-6204162:+
Coord C1 exon
chr14:6202043-6202177
Coord A exon
chr14:6202178-6204058
Coord C2 exon
chr14:6204059-6204162
Length
1881 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TGTGTGTTGTTTGCTTGCAGGAC
3' ss Score
11.36
Exon sequences
Seq C1 exon
GTGGCGGAGTGGGGAATCCGTAAACTGGGCCTGGTGAAGTATGTGGACAAAAACGCTGGAAGCTACAGTGGAGGAAACATGCGCAAACTGTCCACCGCCATATCACTGATTGGAGCTCCACCAGTGGTCTTCCTG
Seq A exon
GTAAGTGGGTATACTCACACACACTTTATTTATATGTATTGCGGGGCTTACAGGGACACTCCATGTATAAGCATACCGCTAAACCCAACCAAACTGGCAAATTTCAAACAATAAAAGCCCCTGTTAAGGGTTAAAAAGCCCCCGTTTTTAAGCATTTTAAATTACAGGGGCACAAGGTGTGACCCTGTACACCAGTGTTTCTCAACCATGTTCCTGGATGACCACCAGCACTGCATGTTTTGGATGTCTCTTTTGTCTGTCACCCCCATTATAGGTCTTTCAGACCTTGCTAATGAGCTGAGGATCTGAATCAAGTGTGTTTTGTTAAGGAGACATCCTCCAGGAACATGGTTAAGATGTTCAGTGGCGTTAGTGATAGTCAGTAGCAATAGTGATGTTCAATGGTGATAGTGATGGTCAATGGTGATAGTGATGGTCAATGGGGGTAGTAATAGTCAATAGCGTTAGTGATAGTCAGTGGCGATAGTGATGATCAATGGCAATAGTGATGTTCAATGGTGATAGTGACGGTCAATGGGGGTAGTAATAGTCAATGGCGGTAGTGATGTTCAGTGGCGGCAGTGATAGTCAGTGGCGATAGTGATGGTCATTGGCGGTAGTGATGTTCAATGGTGGTAGTGATGTTCAATGGTGGTAGTGACGGTCAATGGGGGTAGTAATAGTCAATGGCGGTTGTGATGTTCAGTGGCGGTAGTGATAATCAGTGGCGATAGTGAAGGTTAATGGCGGTAGTGATGTTCAATGGTGGTAGTGACGCCCAATGGGGGTAGTAATAGTCAATGGCGGTAGTGGTTTTCAATGGTGATAGTGACGGTCAATGGGGTAGTAATAGTCAATGGCGGTAATGATGTTCAGTGGCGGTAGTGATAGTCAGTGGCGGTAGTGATGTTCAGTGGTGGTATTAATAATCAATCAGGGTCGTTTTGGTCAATAGTGGTAAAGACAGTTAATGGTGGTAGTGATGGTCAATAATGGTAGTTTTGGTCAATAGCCATAATGATGGTTAATTGCAGTAGTGATGGCTACTGGCAGTAAAGTTGGTCAATGGTGGTAGTGATAGTAATTAGCGGTAGTAATGGTCATTGGTGGTAGTGATAGTCAGTAGCAGTAATGATAGTCAATGGCGGTAGTAAAAAAGTTGTTTTTCTGTTACATTTCTTCTCATATTATTATTATTATTATTTTTTAAGTCTAGCCTATATTAGATGGCATAAGCTAATTACTGTCAGATTTTGACAATTTCTTAAAGCATCTGCAATATGTGCAGTATTTAGTCTTGTATTTCATGTCTTTGTAAAGAATCATTATTTTAATGTATCAGTCAATATTGTTTTAATGTTATGATCTAATCGAGAACATTAACAAGTCCCTTGAATAAATAAAGCAATTCAATCTAACTTCGAGTCCAGCTTTGTTTTGTTTTTAAGCATCTCAACCAAAGCATTTGTAGGAATGAAATCATTCATGATAGTAATATGGAACTGTAATGCGGTCAAGACCTGCCTTGAACTACTCCATCTGTGCTTTTGGATGAGTTATAATTTTGATTGAACAGCCTATATAGCATAAGCTGTAATAATATCTACAGTAATATTCTAATAATTGTTTTACCAATGTGCGATTGTGACACACATCTTGGGTCTATTCACTGCAGCTTGATGCCTATTAGAATGCAGTTAGACCCAATAATTTATAACATATGAAGGCAAAAAAATTGTGTTTTATTTTGATCAAATTAATATTAGTAAAATCGATATTATACAGAATACCCAGAGATCTTCCTGCTAAAGTTGATGTTCATTGTGTTTCTTGCTAACCTGTGGCTGAATCGGAGTCCTGTTGTGTGTTGTTTGCTTGCAG
Seq C2 exon
GACGAGCCCACCACTGGGATGGACCCCAAAGCACGCAGAGCCCTGTGGAACTGCATACACAGCGTCATCAAAGAGGGCCGATCTGTTGTTCTCACCTCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:43
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=FE(30.3=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(2.8=11.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCGGAGTGGGGAATCC
R:
CTGTGTGAGGTGAGAACAACAGA
Band lengths:
238-2119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]