RnoINT0009951 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69902131-69903542:-
Coord C1 exon
chr5:69903338-69903542
Coord A exon
chr5:69902245-69903337
Coord C2 exon
chr5:69902131-69902244
Length
1093 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
TACCTATGCTTTGCTTTCAGGAC
3' ss Score
9.88
Exon sequences
Seq C1 exon
AGCCTGCTGTCTCCTGTGGCTTTTGGATTCGGCTGTGAGTATTTTGCTCTTTTTGAGGAGCAAGGCATCGGGGTCCAATGGGACAATCTCTTTAAGAGCCCAGTGGAGGAGGATGGCTTCAATCTTACCACCTCAGTGTCCATGATGCTGTTTGACACCTTCATCTATGGCGTGATGACATGGTACATCGAAGCCGTCTTCCCAG
Seq A exon
GTACCCCCAGCTTCCATATTGCTTTGGCTAACTGATGGGGAAGGCAGCTTTCTGTCTGTAGGTCCTTCCTTTCTTTGTGTTGCAGTTGCTGAAGGATGAGGGAACTCCCCGGGAGTTGGCTTGGTCTTTAAGCTTGTGTAAAACAAATAGTCCAAGGAAAGGCACCTGTGTTGAAAGCACATGTGTCACTACCACTGTGCTACTAATCTCTAGAGCCTAGTGTGCCAGGTGCCGAGCAAAGTACTTTAGGGGCTCTGGTTCGGAAGGTTGCTCTGGACTGTTTCCTATTGTAAACAGTTTCTAAGAGAGAGATTTAACTGAGAATTTAAGCGACTTGCTAAGGTCATGTGTCTGTTAAGTGTCAGTGCTTGGGGATGACCTCAGCTGGGCTACACTAGGTCAGAGTCCGGCAGGTTTCTCTTAGTATTGACTGGGTTCTTAGTTCTATGTCCCCAGAAGAAGAAGCCCTAGGAGAATCTATCTACTAACTACAGGCTATAAATAATATAATGTATTGGGTCTCGGCTCTTACCCATGGCTTAAGGCAAAGTAGTATTCACCAACAGTTAATTCTGATGCTTTTCTAACCTTCACCAAGTACAGCAGGACCCCTCTTCAGGATACGTTTCTGTCTGAGAACGGATTTTAGGGAGAGTGAAGTTAGGCTCATGGCCACCCTTTGACTCTCTTCCAAGGAAGCTCATTTGTAATTTTGTTGTTGTTGTTGTTGTTTTAAACCCATATCTGAACTTCCTCCATTGACCATGCAATTTGCATGTATAGATAAAGATTCAAATTCAGAATCCTTTTTCTTTTGTGTAAGTGACCTTGGATATAGCTACTTGTCCTGCCCTTTGCTCATCTCTCAAATGAGGATGCTATTACCACCTGGGGAGTTGTTGGGAAGCCATGGAGAGGTGCAGAATATATGATTTGTACAGCAGGTTTCGGCCAAGAGTTAGCTGTCTCCCTCCAGTCCGCTCCTTCCCCATAGGGCGTGCTAAGGAGAAAGAGGGTCTGGCTAAGAAACGTCAGAACCGCTGAGATTGCGTCAGCTGGGGTCATGCCTGTGCTACCTATGCTTTGCTTTCAG
Seq C2 exon
GACAGTACGGAATTCCCAGGCCCTGGTATTTTCCTTGTACCAAGTCCTACTGGTTTGGGGAGGAAATTGATGAGAAGAGCCACCCTGGTTCCAGCCAGAAGGGTGCGTCAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:17
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=0.205
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(13.8=88.4)
A:
NA
C2:
NO
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:
AGCCTGCTGTCTCCTGTGG
R:
TTTCTGACGCACCCTTCTGG
Band lengths:
319-1412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]