DreINT0023503 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51959380-51960434:+
Coord C1 exon
chr1:51959380-51959496
Coord A exon
chr1:51959497-51960239
Coord C2 exon
chr1:51960240-51960434
Length
743 bp
Sequences
Splice sites
5' ss Seq
CGGGTGCGT
5' ss Score
7.91
3' ss Seq
AATTGTTTTTTCCTCAACAGACG
3' ss Score
9.18
Exon sequences
Seq C1 exon
GTCAATAAGACGTTTCAGGAGCTCGGTGTACTCCGTGACCTCGGCGGCATGTGGGAAGAAATGAGACCCAAAATCTGGAACTTCATGGAGAACAGTGAGGAGATGGACCTCGTCCGG
Seq A exon
GTGCGTCACATACACACCCACACACACACAAACACACACACAAACACAAACACAAACACACACACAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAGTCTTTGTGAACGCAGATAACCTTCCTGAAACACCACACGGTTCCTGTAAGTGTCCTCTGAGCACATGATGATGTTGTAGGAGTAGTTGGGCATGTGTGAGTCACACCGCCACCTTCAGGACACCAGCAGTTCTGCGCTTTAGCCTCTGCTGAACTCACATGGCTCTCAACGTGTGCAGCGCAGCGGGAGAACATATATTAGGAGATCTTCAAACCCTCGGGAGTTCACAGGACTTATCTGTGCCCAAAAGAATGAAAAAGAGCATTATTTTCAGTGTTTTGTTGTCATAAGCACAGAATGCATGACTCGCCGTCGTATGACTTCATGTAAGGTCATGCTGACAAATAGAAATAGTCACAACAGTCATTTAAATTTGACAGAAAGTGCATTTAATTAATATAGAAAGTAATATTTTTTCACAGTATACATGTATGAATGGGATATAATAGAAAAGGCTTCACAGCATATTTCACAGCTGCATGAATGCATTAATTAATCTGATTAATTCACTAAATTATAATATAGCATCATATCATAATATTATAATATAGTCTTTTACGACTACAGGAGATGCATGGTATTTCTGATATTAAACCAATTGTTTTTTCCTCAACAG
Seq C2 exon
ACGCTGCTCCAGAATAACGCCAGCGCTCGTTTCTTCAATGCTAAGCTGAGCGGGACAGAATGGCGCGTGGAGGATGTGTCCCGCTTCTTGTCCAAGTCTTCAGAGGACACTCGTCCACATGGGACAGCGTACACATGGAGAGAAGTGTTCAACGAGACTGACCAGGCCATACAGACCATCTCCCGCTTCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:10
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=0.046
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(4.5=24.6)
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:
TCAATAAGACGTTTCAGGAGCTCG
R:
TCCATGAAGCGGGAGATGGTC
Band lengths:
310-1053
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]