RnoINT0009984 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69863681-69864949:-
Coord C1 exon
chr5:69864815-69864949
Coord A exon
chr5:69863785-69864814
Coord C2 exon
chr5:69863681-69863784
Length
1030 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTCTTTTATTCTAATTATAGGAT
3' ss Score
8.26
Exon sequences
Seq C1 exon
GTTGGTGAATGGGCAATTCGCAAACTGGGCCTTGTTAAGTATGGAGAAAAATACGCCAGCAACTACAGTGGCGGTAACAAGCGGAAGCTTTCCACAGCCATTGCTCTGATTGGCGGGCCTCCTGTGGTGTTTCTG
Seq A exon
GTGAGTGTGAGGGGGTTGTGCGTGAGTGCAGGGTGGAAGCTGTTCTTCTGTCTAGAATAGACAGCATGGTTTATCCGAAAGTCACATATAGGCCTTTGCGTGCCATATGCGTGGCATGGCGACAGCAAGTCAATCTGCCTGTGGCTCCAGAACAGGCTCGGAGAATCCAGAGGAACCTTCTCCCACAAAGCACACTGGGTGGCTCTGTTGTACCTTCACAGGCTCCCCAAGTGGACAGGCTCCAGGCATCTTGTTTCCTTGCCTCAGATAATCGCTACAAACACGGCTGAAGCTGAGTGTGCCAATTGATCTTTCTCCAGAATGTTCTCCATGACTATATATGTTCATTCTCCAGGGTCAGAAGTGAGGACACGGCTCCTGGAGGAGCCATAGGATCAGAGTTGCTCCCATACAGATAAATAAAAACCAGATCAGACTGCGCAAGTGGTCCTTGATCCTCATCTTATAGAGAACACTGAGGGTATGGGAAGAAGCCTTGGGTCGAAGCTTTAATTTTTATTGACCATGTGGATACGAAATTTCTCTGTGATTAGCAAGTGTAATAGAACAAGGAGAAAAATATGAGCATCAATTTTACCCAAACACTACTCAGACTTCAAAATGGTTTTGGACAAAAAGTTGTGATTTTGTTGTAGTTTTGTAATAGGGTTTCACTATGTAGTCCTAAAACTTACTATGCAGACTAGGCTGTCCTTGAACTCACAGAAACCCACGTGTCTCTACTCCACACCATACTGGGAAACCCAGCATGATCTTTAGCATTTAAAACAAACAAACAAACAAACAAACAAACAAAACTGTCTTGGACTGGAGAGATGGCTTAGTGGTTAAGAGCATGGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTCTAATGGAATCTGGTGCCCTCTTCTACAGCATACTCTCATCTCTTAAAGAAATTGTCTTTGATATTCTTTCCTAGCAAATAATTAAACTTCTTTTATTCTAATTATAG
Seq C2 exon
GATGAACCAACCACAGGCATGGACCCCAAAGCCCGGAGATTCCTGTGGAATTGTGCCCTAAGCATTATCAAGGAGGGAAGATCCGTAGTTCTTACATCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:47
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=0.029
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(30.3=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(2.8=11.4)
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:
GTTGGTGAATGGGCAATTCG
R:
CTATGAGATGTAAGAACTACGGATCT
Band lengths:
239-1269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]