RnoINT0009946 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69907940-69909021:-
Coord C1 exon
chr5:69908824-69909021
Coord A exon
chr5:69908146-69908823
Coord C2 exon
chr5:69907940-69908145
Length
678 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GGTTTCCTTCTGTCTGTCAGTGT
3' ss Score
6.78
Exon sequences
Seq C1 exon
ACGATGTTGGACAGCAGAGGCAATGACCAGTTTTGGGAACGAAAGTTGGATGGATTAGATTGGACTGCCCAAGACATCATGGCATTTCTGGCCAAGAACCCAGAGGATGTTCAGTCCCCAAATGGCTCTGTGTATACATGGAGAGAAGCTTTCAATGAGACCAACCAGGCAATCCAGACGATATCTCGATTCATGGAG
Seq A exon
GTGAGGGTCTGCTGTGCACACCTTTTAGCAAAGTCTGGGGCCTTTTTTCCTTTGAGCTGTTGCAATAGTTATAGGCAGAAGGAGAGCTTAGAACGAATGTGTAGTGTCACGTACAGCTATATTCTGCAGGCCTGGCGAGCAAGATAAACACTAGATGAATGGCTTAACGAGCGAATAAGCTTACGTCTAGCTTTGGTTCAGATCGACCCCAGTGTTTCTATCCTTATCTTCTAGCTTTCCCTCTGTTTTGATATTCTAGATCCTAATGATAAACTGCTCTATTATAAAGGCATTATTTATGAAACTTATCTAATCTAATTTGGGACAGATAAAACTTTAAATCTTTAATCCTAAAAATGATGGAAAGAGAAAAGGCTGAGTAGAATCTTTTCTTATCTGATTTCTAGTTGCTTAGTCGCGGTGACTTGACTTTGCTAAGACATGTTGCTAAGAGAATAAAAATTGTTAAAGAGAGTCATTCCCTCACACAAAGCAGTATAAGTAACTTTCAGTGTTCCACTCAAATCTCAGTTCTAAGCTTGGCTGAAACCTGGAAGACTACGTTAGAGACGGTACAGATTAAGAATACAGGCGGCTAGTTCCTGCCTCTCAAAGGAGGCTGAGTACTGCTTGTCTTTCTGGTTGCCAGTTCTAATGAGGTTTCCTTCTGTCTGTCAG
Seq C2 exon
TGTGTCAACCTGAACAAGCTGGAGCCCATCCCAACAGAAGTCAGGCTCATCAACAAGTCCATGGAGCTGCTGGATGAGAGGAAGTTCTGGGCTGGTATCGTGTTCACAGGAATCACTCCTGATAGTGTGGAGCTGCCCCACCATGTAAAGTACAAGATCCGGATGGACATTGACAATGTTGAGAGAACCAATAAGATCAAGGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:12
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=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(14.7=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(15.3=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:
TTGGACAGCAGAGGCAATGAC
R:
CTTTACATGGTGGGGCAGCTC
Band lengths:
342-1020
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]