RnoINT0009947 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69907217-69908145:-
Coord C1 exon
chr5:69907940-69908145
Coord A exon
chr5:69907394-69907939
Coord C2 exon
chr5:69907217-69907393
Length
546 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
CACCTGAGGTTTGGTTTCAGGTA
3' ss Score
5.38
Exon sequences
Seq C1 exon
TGTGTCAACCTGAACAAGCTGGAGCCCATCCCAACAGAAGTCAGGCTCATCAACAAGTCCATGGAGCTGCTGGATGAGAGGAAGTTCTGGGCTGGTATCGTGTTCACAGGAATCACTCCTGATAGTGTGGAGCTGCCCCACCATGTAAAGTACAAGATCCGGATGGACATTGACAATGTTGAGAGAACCAATAAGATCAAGGATGG
Seq A exon
GTAAGGTGAAACGCAGTCTTGCAAAGCTCAAGAACGTAATTTGGATGACTTTTATGACTGGTGGTTCTTTATTGAGGAATGTCAACAACAAATCAGCCACGGCATGACTTTGGTAAAACTCCATTGCTGAGGACTGTTATACAAAGGCTATAAAATATTAGTCTTTCTGTTTCCATGTTCCTGTTCAAAAGACTAAGCTAAAGGACTTAAAAGTCAGGAGAAAGAAAGGAAAGCCATTAGGTCTCCTTGCTAGCCATACATATTTTTATAAGAAGAGGCAGACAGCTTGTAAGGGAATTCCAGTATGTCCAGCAGATGCAGTGTTAGTCACTAGTAAAGTGAAAAGAAAAAATATACCCATAAGGAGTATGGATATATATAAGGAGTGTCCATTGTGACTATTTCTAACCAAGAATCTATGTACTTGTCAACTGTGATAAGAATGGGAGATAGAAAATAGGAAGAGTGGCCAAGGAAGTGTGGGGGAATTGGATTTTTCAGGGTGTGCTTTGTAGGACTGTTTCGTCACCTGAGGTTTGGTTTCAG
Seq C2 exon
GTACTGGGACCCTGGTCCCCGGGCTGACCCTTTTGAAGATATGCGCTATGTCTGGGGTGGCTTCGCCTACTTGCAGGATGTGGTGGAGCAGGCGATCATCAGAGTGCTGACGGGGACTGAGAAGAAAACGGGCGTCTATGTGCAACAGATGCCCTACCCCTGTTATGTTGATGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:13
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(15.3=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(13.3=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:
TCCCAACAGAAGTCAGGCTCA
R:
AACAGGGGTAGGGCATCTGTT
Band lengths:
342-888
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]