DreINT0023562 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6180676-6181849:+
Coord C1 exon
chr14:6180676-6180815
Coord A exon
chr14:6180816-6181711
Coord C2 exon
chr14:6181712-6181849
Length
896 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
TTACTTTTGTTGTTCCTCAGGTG
3' ss Score
11.37
Exon sequences
Seq C1 exon
GTTGACAGTAGAAGAGCACATCTGGTTCTATGCTCGCCTGAAGGGTCTGTCTGAGGAAGAAGTGAAAGCTGAGATGGAGCAGATCCTGAGTGACACTGGCCTTCCGCACAAACGCAAATCCAGAACCAGCCAGTTGTCAG
Seq A exon
GTTGGTGACTTTACCTGTTGCATGAAAATCCTTAAGCTAGGAAATTTCTTAGTTTGAAGGTTAGGGGTACCCTTAGCAAAACTTGGGTCCCAAGAACAAAAACCTAAAGGTCAACTTAAGGACTTTAAGGCTGCCATTAAGTATTTCCTCTTAATGATCTAAGTCAAAGGTGTCAAAGCCAATTCCTGGAGGGCCGAAGCACTGCACAGTTTAGATCCGACCCTAATTAAACAGTCCTTCAGGCTTGTTTGAAACATACAGGTAAGTGTGTTGAAGCAGAGTTGTAACTAAACTGTTCGAGGCTGCAGGCTTCCAGGAACTGACTTTGACACCAGTGATCTAAGTGTTCCCTTAACCATTGCAAAGTTCTTAGTAACCCCTTAAAATTTTAAAGGAACTAAAACAGCTACCTTAAATGGGCAAATGACCCATCACAGGAAAACATAGCTAAATATACACAGCGTGTCGAAAACACGTCTGTCCAAAAGGATCTACGTGATCCCAGCTAAGTTTAATAGGTCCTTCATACATAATGTCGAGATCAATTAAATAAGGGAATGTCTCGACTTGCTTGATGAAAAAATTAAACGGCACAGATGATGTGTATTGCAGAGTATACAATCTTTTAACTATAGCAACCACGACACCCTTATGTCCTATGTTACCAGAAACTAAAGTGAATCACTTACAAAAGTCACTTAGGTAAGGGTGACAGTTAAGAAGTTTGTTACGATGCTCTAAATGAAATCCCTTCCCTCAGGGATTTCCCCCCTCAGAGACACCCTTAAGTTACTTTCATTCTTTTTATCCTTAAGGACTTTCATTCAACCAGGCACTGAACTTTTGTTTGTTGGTAGGTTTTATTGGTTGCAAACCTTACTTTTGTTGTTCCTCAG
Seq C2 exon
GTGGTATGCAGAGGAAGCTCTCAGTAGCTCTTGCTTTCGTTGGAGGGTCAAAGGTTGTCATTCTGGACGAGCCTACTGCTGGTGTGGATCCATATGCTCGTAGAGGCATTTGGGACCTTTTATTGAAGTACCGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.208 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(17.9=55.3)
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:
GTTGACAGTAGAAGAGCACATCTGG
R:
CTGCACGGTACTTCAATAAAAGGT
Band lengths:
278-1174
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]