RnoINT0009964 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69888616-69889914:-
Coord C1 exon
chr5:69889790-69889914
Coord A exon
chr5:69888715-69889789
Coord C2 exon
chr5:69888616-69888714
Length
1075 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGTCTCCCATGTGACTGCAGTAA
3' ss Score
4.89
Exon sequences
Seq C1 exon
ATTGTCCTGCCGGCTGTCTTTGTTTGCATCGCCCTGGTCTTCAGCCTGATCGTGCCACCCTTTGGCAAGTACCCCAACCTGGAACTTCAACCCTGGATGTATAACGAGCAGTATACATTTGTCAG
Seq A exon
GTATGTCTGCCCTCTGTGCCTCAGGGCAGAGAGGCTTGAACCAGGACATCAGCGTTGCTGTACTGAGAGCCGAGGAGTCAGAATCCACGGTTCTGAGGTGGAATGGTTTTCTCATGATGGCTCTGGCTCCTATAGAAGCCACTGCTGCAGCAAAGGGCAGTAATAAACGATAACTTGAAATTCCAGGTTTCCTCTTGTATTGTTGGGCTCTTGTTGTCAGGAATGACCAGCTATGCATAAATTCAGTAATCACCAAATCTTTCAGGTTAGGATGCTAGCTAAGTGTGTGTCTTTAGGCAAGAATGCTTCCTATTTCATACTGGTCCTATTAAAAATCAAAAGATAGAGGACTGTCTAACCTTGTTTAGCACAGATTTTCTTCAGGTCGGATGCACTGGTAGGTCTGCAGATGGGAGAAAATGTCAGTGATAGAGAGGGCAGTTTTAAAAGGATTAAAAATCTCTGTGTGTGCATGTGTGTAGGATACGTATATATCATAATAGATCGCTTATTAGCCTCTTCTGCTCTAGCTCACTTTCATCCTATATGGTTGAAAGTTTGTTTGATCCGTTTCTAGCTGATGACCTAGTATTGCCCATAGCTACAGATCATGACATTGGTTTGTGATCTAGGCTCACTATTTCTTGGGCTTTTTAATTGTTCATACAAGTAATCAATAAAATCTTCCTGTCTGTTCTTAGAAACTTCTAGTTGTCAGTGTCGAGTGGTAATTGTCAATGTAGTTTTGAAATACTGATCCTTAATGATTTTACTTCAAATGAAGGGTATGTGCATTTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATGCATGCCTTCACTCTGTACATGATTCATTGGGGGTATTGTATGTTACCCTGATGCCAAGTGTTGGAAACTCCTTGCAGATGACTTCTGTGTATTACTTATTTTAGCTTTAGAAGCTTGTTCCTCAGAAAGTGCTTAGTAGAGTTTTATCTGTAGAAAACGTTTCTTGCCTCCAAGTCCTGGTTTGGATGAATTACTGATCTGAATGTCTCCCATGTGACTGCAG
Seq C2 exon
TAACGATGCTCCAGAGGACATGGGCACCCAGGAACTCCTCAATGCTCTAACCAAAGATCCAGGCTTCGGGACCCGTTGTATGGAAGGAAACCCAATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:29
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=0.206
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(7.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(6.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGTCCTGCCGGCTGTCTTT
R:
GGGATTGGGTTTCCTTCCATACA
Band lengths:
224-1299
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]