RnoINT0009953 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69899490-69900697:-
Coord C1 exon
chr5:69900526-69900697
Coord A exon
chr5:69899622-69900525
Coord C2 exon
chr5:69899490-69899621
Length
904 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGA
5' ss Score
5.58
3' ss Seq
TCTGTTACTCTTGTCCTCAGGTC
3' ss Score
10.9
Exon sequences
Seq C1 exon
TCTGCATGGAAGAGGAGCCCACTCACCTGAAGCTGGGGGTATCCATTCAGAACCTGGTGAAGGTTTACCGAGATGGCATGAAGGTTGCTGTGGATGGTTTGGCGCTAAATTTTTACGAGGGCCAGATCACCTCCTTCCTGGGCCACAATGGAGCAGGGAAGACCACCACCAT
Seq A exon
GTAAGAAGAGGGTGTGGCTCTCCCAAGATCTGCCACAGGAAATCCCCACTTAGAAGCATACACCTAAGGCTAAGAGCAGAGCATGATGGGAAGAAATGTGTCAATCATGAGCATGCCTTCTGAGGTCTAGATTTTGCTAGGTGTTTTTCCTTTAGTCTAAAATAGGCAGGAACCTTTTGATGAGTTTCCCCATGCAGTTCTCAGAATTCCCCAGCTTTCTTGGAATCTGAGGCTATCTGTTTCTGAACTCGTTGGTTCAGAGATTTGAAGCAAGAGACTGGAAAGAGATCAAACAAGCTAGAGGAAGACGGACACTTCTAGAAAATCTGACTTCAAGCAGATGAGAGAAGGCCTGGGTAGCTCTCTTCCTCTGCCTTCCCTGGGACCTGTGAGGACAGAGGAAGGGCCATAGAATACAGTAGTTTGCTTACAGTTTGTAGTGTGGTCCCTCTGCCATTTCTGAGGTTGATCTTTGGGGATGACCAGCTTTCTTCTTCAACATAAAACCAGTATACTATGAACATGACTGAGATACTCAGGAATTCTGTTATGCAGCACAAACATTTCTATCTTTTAACAATATGTTCTTGCTTATTCTTTTTTTTTGTACAGAATGTTAGGCATACAAAATATGTTTTAAGGAGCACACCCGTTTGCAAATTAAGAGTAACATTTTCAGTTGCTCCTAGCAAACTCCTATCTCTAAGACATAGGCTCATGCTTAGCCACTCACTAAAGCAAATGGCCTCTTTGCTCTGTGGGCATCTATTAGATTGGATTGGATTAGATTAGAAAGGAAGGGATAGAGTGTGTTGTGTGATCTGCTCTTTTTGCCCTGACTCTGCAGCACTGAATGGTAAGGCTGGGTCGTCCTGATTCTTGCATCTGTTACTCTTGTCCTCAG
Seq C2 exon
GTCAATACTGACTGGGTTGTTTCCCCCAACTTCTGGCACTGCCTACATCCTGGGGAAGGACATTCGATCTGAGATGAACTCTATCCGGCAGAACCTGGGAGTCTGTCCCCAGCATAATGTGTTGTTTGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(18.5=46.6)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.1=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:
TCTGCATGGAAGAGGAGCCC
R:
GTCAAACAACACATTATGCTGGGG
Band lengths:
302-1206
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]