RnoINT0009952 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69900526-69902244:-
Coord C1 exon
chr5:69902131-69902244
Coord A exon
chr5:69900698-69902130
Coord C2 exon
chr5:69900526-69900697
Length
1433 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTCCTTTCTTCTGTCACAGTCT
3' ss Score
10.18
Exon sequences
Seq C1 exon
GACAGTACGGAATTCCCAGGCCCTGGTATTTTCCTTGTACCAAGTCCTACTGGTTTGGGGAGGAAATTGATGAGAAGAGCCACCCTGGTTCCAGCCAGAAGGGTGCGTCAGAAA
Seq A exon
GTAAGTACTGCTGACCAGAAATATCCCCCCCCCACCCGCTGTGGAGCAGAGCCTGTGTCTAGCATTTAACATCACCCCAAAGCCACAATCGATGGGGAGAAATCCCATGCAGTAGGTCCTTTCCCAATGCACCCATGCCATTGCCATCCCACGCACCTAGTGGGAACCATATCTGTCTCCTGAGGAGAAGTTCTTTTGTCGCCCCTCTTCTAGCAAAGTATATTTTGATCAGTATACCCTTATTTCTCCATCTAGGATAATCATGCTACTCTACTAAGCCAAGAGGAATAACTACAGTTAGCCATCGTTGTGGACCTAGTTAGTTTCTCTATCTGCCTTGCTGTGGTGGTCTATCCTAGGGATTCTGTCGGTAGATACCAAGAGGCTGCTATATACCCAGCCTGGGCTTCATAATTTCCCACCCTTTCTCAAGTAGGGTGCTAATCCCCTCCTCGCTCCTGACTGCAGGTAGAGGTGCCCCAGTTCTTCCCAGGTTTTCTGTTTGTGTCTTTGTGCTCAGTGTGGCTCCCTTCTCCATTGTCAGTGGCCCGCTTTCTTCCTGTGTTGTCAGTAGATCTGCTACCTCTCTACATTGTCAAGGAGGCCTGCTTCCTCCCTGTGCTCTCAGGGTCTCTCTTCTGTGTCCTTCCCACTGGTTGCCTTTTGGTGCTCCTTAGTGTAGATAACATGCAACTTTAAAATTTTTATTTTATTTTTTTTATTTATTCCTTTTACATCACACTCACTGCCCCCTCCCTGTCACCTCTCCCCTCAATCCCTCCCCCTTCTCCTCTGAGTGCATGGGAGCATCTCTGGGTATCACCCCCACACTTAAAGTCTCTGAGAGGCTAGGTGATTCCTCTCCCACTGAGGCCAGACAAGGCAGCCCAGCTAATAGAACATATCCCACCATGTGTGTACAGGCAGCAGCTTTTGGAATAGCTCCAGTTGCTGGGGAACCACATGAAGGCCAAGTTGATTTTTTGGGAGGGAGTGGATGGATCTTTTTCTCGATTGGTATAATTCTTTTGAGATCCACTCAAATTGTGATATATTTAGTTCATTGCCATTTTTGTTTGTTTGTTTGTTTTTCCTTAATGAGTACTGTTGCATAATACGGGTATCCATGACACTTTTAGTTTATTTTAATGTTTTTCTAAAATGTCTGTTAGCATCCTGTATTTTAATTGTTTGTGCAGCCTTTCTTCATCCACAGACTAATGGTTTTTTTTTTAATAAGTCCATTTCGTTTATCAACATGAGTGTCCCAAGAGGCTTAAAATATTTCATCTCCTGTTTGTCTGCAACATTAAAGGTTGAACACAGACAGAAGCTAGTTCTAAAGGTCTAAGCATAGACGTTTGTATTTCTACACTCTATTGGCCAGGTGTGTTTCCTGCAGGATCATCTCTGTCTCCTTTCTTCTGTCACAG
Seq C2 exon
TCTGCATGGAAGAGGAGCCCACTCACCTGAAGCTGGGGGTATCCATTCAGAACCTGGTGAAGGTTTACCGAGATGGCATGAAGGTTGCTGTGGATGGTTTGGCGCTAAATTTTTACGAGGGCCAGATCACCTCCTTCCTGGGCCACAATGGAGCAGGGAAGACCACCACCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.205 A=NA C2=0.017
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(18.5=46.6)
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:
GACAGTACGGAATTCCCAGGC
R:
ATGGTGGTGGTCTTCCCTGC
Band lengths:
286-1719
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]