RnoINT0009944 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69912784-69913371:-
Coord C1 exon
chr5:69913232-69913371
Coord A exon
chr5:69912901-69913231
Coord C2 exon
chr5:69912784-69912900
Length
331 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GGTTCCCTACCTGACTCTAGGTG
3' ss Score
6.74
Exon sequences
Seq C1 exon
CTCCTTATTGCAATGATTTGATGAAGAACTTGGAGTCTAGTCCTCTTTCTCGAATTATTTGGAAGGCACTCAAGCCACTGCTCATTGGGAAGATTCTGTATACACCTGACACACCAGCTACAAGGCAGGTCATGGCTGAG
Seq A exon
GTAAGCTGTTCAGCCTTCGGACTGTGTCCCCGGAGTCCTCCCAGACTTAGGAGTAGGAAGCCTCAGATAGAGTATGCTGGGTATATTTTTGGTCGTAATGGGACTCTTTAAATAGTCAAAACCAAACTGAACCAAATCCACATGTAATCTTGGGAGCCACATCCCCAGCCCTGAGTGTTTGAAATATAGCTATAGGACAGATTGCCTGAGGAAGTAAAAGGACTGGGCAGAGTTTTCTGGAATAGGTGGTGTTTTTTAGGCAACCTCTAAATGTTCGACACCTCTGCCTCTCTTGTGTTTGTATGAATCCTGGTTCCCTACCTGACTCTAG
Seq C2 exon
GTGAACAAGACCTTTCAGGAGCTGGCTTTGTTCCATGACCTGGAGGGCATGTGGGAAGAACTCAGCCCCCAAATTTGGACCTTCATGGAGAGCAGCCAAGAGATGGACCTTGTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.026
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(8.6=97.4)
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:
TCCTTATTGCAATGATTTGATGAAGA
R:
CCGCACAAGGTCCATCTCTTG
Band lengths:
256-587
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]