RnoINT0009978 @ rn6
Intron Retention
Gene
ENSRNOG00000018126 | Abca1
Description
ATP binding cassette subfamily A member 1 [Source:RGD Symbol;Acc:631344]
Coordinates
chr5:69869997-69871544:-
Coord C1 exon
chr5:69871421-69871544
Coord A exon
chr5:69870127-69871420
Coord C2 exon
chr5:69869997-69870126
Length
1294 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
GTTTGCATTGTATCTCACAGGGG
3' ss Score
8.42
Exon sequences
Seq C1 exon
AAATTCAATGACATCAATGACATCCTGAAATCTGTGTTTCTTATTTTCCCACATTTTTGCCTGGGGCGAGGGCTTATTGACATGGTGAAAAACCAGGCGATGGCTGATGCCCTGGAGAGGTTTG
Seq A exon
GTGAGTAAGGCAGTGCAAAGCTTTGATGGAGGTGTGTTAGTTTTCCTGGGCCTCAGCACCCTCATCGCTGCTTCAGAAAGGGGCTGGGTACAGGATGTCTGTCCTTCCAACTGTCATGGGCCAATACCAACACAGCTGCTCTGTCTGTCATGACAGACACCCATCATATAGGTGTTTATCTGTGCCTCTGACAGCACTGAGATAAATGGGGGAAATTTTTGGAAGCAGGAAAATGCTGGCATTTGTTTGAAATCAATTCCTGATGCCACTGGGTGAGCTTGTCAAATCACTGGAAAAATCAAACCACAGCTTTGGCAAATAGATAAGGACAGATAGTCAAAAAGAAAGATATACCCTTTGATTCTACTAAGAAAATGTAGGCCTTCAGTGTAATTTATTGAAGCTTTCTTTTCCCCCTACATTTATAATGATTAAAATATCTCCTGCTATTATGTGACTATTACTCATTTGCTGGTTAATTGAGTTAAATGGGCCGTGCCACTTAAAAACATAGAAGAGGATGTTTTCAGTTTAGTGATACAAAAGAGACATGAAGGATTAAGGCTATTAATCTAAAAAATCATCCAATTAGGTCACCAGGTTACGTTAAATGCTGCAGAAATGGGCATTGTTTGAATGCGTTTTCTAATGCCTGTTACTTTGAAAACTTAGAACTAAACAAAACCTGACTCCTAAAATTTCCCAGGATTATTGACCTTACTAGACTTGATTCATTTGAGTTTCGGTGGGGTCATGTCTCATTAAAAAGGGGATTTTAGCAATCTTAATGAACTTACAGATCTAATGCTAATTGACTCTAAAATTCTGACCTGATACCACCAGGTTATATTATAGTTTTCCAGATGAAATCTCAAAAGTAGACACTTTTTTCTTCTTGTCAGGGGTGGTGTTTCTAGAAAAGTTATATGAAATTGGCCCCAAAATGAAGAAATCCTTCCCTCCCTTCTCCTTCCTTCCTCCCTTCCTCCCTCTTTCCCTTCCTTCCTTCCTTTTTTTTTAATATAAAGGGAGTCCTTTAATATTTCAAGAGTGAAAAAAACCCCAAAAAAGTACATTTATTTACAATAATCTAGTCTTGAAAGTTAAGCATAATATTAACTAATTTAAATGAAAAAAAGCAGTCAAACAACAAAGCCAGGCCCAGCTTAAGGGCCCTCTCTGTGCAAGCACTATTCTGTGTACACAAAAAAGGACCCTCATCTCAGAAACAGGAAGTGGGGCCATGATTTCCGAAGCCTCCCCTCTGACCAGATGTTTGCATTGTATCTCACAG
Seq C2 exon
GGGAGAACCGCTTCGTCTCTCCACTCTCTTGGGACTTAGTAGGACGGAACGAAAATGCCATGGCCGTGGAAGGGGTGGTGTTCTTCCTCGTTACGGTTCTAATCCAGTACCGATTTTTCATCAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018126:ENSRNOT00000024564:41
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(7.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PD(6.3=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATTCAATGACATCAATGACATCCT
R:
CTGGGCCTGATGAAAAATCGGT
Band lengths:
254-1548
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]