RnoINT0010406 @ rn6
Intron Retention
Gene
ENSRNOG00000004040 | Abca8
Description
ATP binding cassette subfamily A member 8 [Source:RGD Symbol;Acc:1307069]
Coordinates
chr10:98261668-98263717:-
Coord C1 exon
chr10:98263551-98263717
Coord A exon
chr10:98261802-98263550
Coord C2 exon
chr10:98261668-98261801
Length
1749 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
TATGTTGAATTACATCCTAGAGG
3' ss Score
3.77
Exon sequences
Seq C1 exon
GCTCTTGGTTCTGGGAGTTGCCCTTTGCCCTCTTCTTTTCGAAAGTATCAAGATGAAAATACTTCAGAGCGCTTACACTTGGGATCTTTCCCCACACTCGTACTTCCTTGCCCCTGGACAACAGCCCCACGGCATGCTCACTCAGTTACTGATCATCAATAAGACAG
Seq A exon
GTAATAACATATTTCCAACTCACATGTGTATCTGTATTTCATTCTTAAAGTGCCGAACAAGAACTTAGGATGGGGAGCATACAAGAAAAGAAAGGTCAAAGGTAGCAGAAGGCAGAGGCAAGGAAAAGGAGAATCTACTGGAAACACATTTCATTCAACAATACCACAGAGATGTCTGAGATCTTATAGTCTCATTTTAATCATTTAATTACAGTGTTAAAGAGTATTCTACTGTGTACTTATACCACGTTGTGTCTATCAATCACCTGTAAATGGATCCCCCCCCACACAAATGGTTATGAATAGTACTTTGATCATGAACAGTACTTTGATCGGTGATCGTGTGTATTTTTGTGAAGATCTTTTTTCATTTCTTTGGGGTATCCTCTTAGAAGTGGGATTGTTGGATCATATAATGCAGATGTTTAAACTCTTAAGGACCCACCAAATTGTTTTCAAAGTAAGTGTACGTGCATGCTAGCAACATATGCATTCTAACTCCTGAACCCCTCGGATGATTCCCCTTCCTGACTTTTTATAAATATTGCAAATGTCCCACGATATCTTCTGTCTTGTGTGTATGCATTTCCTATGTTTGCACATGTCTTTGTAAACAAGGGTGTGCATGCATGAGTGTGCAGGTAGAGGCCAGAGGTCAACATTGGATGTTTCCCTCAGTCATTCTCTACCTTAATTTTTTTTGTTACTTTCATTTTTTTTTACAGTCCAATCATTGTCCCCCTCCTGGTCCATCCTCCCACAGTCCCTCATCCCATTCCTCCTCCCCACTGTCTTCAAGAGGATGCCCCCCACTGCCAGGCCTCCTGACTCCCTGGGCCCTCAAGTCTCTAGAGAGTTAGGTGTGTCTTCTCCCACTGAGGCCAGACCAGACAATCCTCTGCTGTGTATGTGTCTGGGGCCTCGGACCAGCTCATGTCTGCTACCTGATTGGTAGCTCAGTGTCTGAGTCACTGAAACTTGAACTCATTACACTGTCTCTTCAATGAGCTCAAGAGATCTGCCTGCCTCTGCCTCCCAATGCTGGTATTGCACACACATGCCCACACGTCTGAATTTTTGTGCAGGTGCTGGGGACGGAACCTAGGTCATCACCTTGCTCAGCGAGCACACATGCTCTTGACTGAACAACCTTCTCAGTCCTTTTTTCTCTTCTGGTTTCTATTTGTGTTTTTGGTGCTGAGGGCTCTTCTCGTGCACTCACTGACTTTCTCAGAGATGTGTTCTCGCCAATTTTAGTAGAGTTCCTTAAGTATATGTTTCTTCGTTTTCTGCACATGCCTAGGCGAGTTCCGAGAGTTACACACTGGTTGCTTATCTGGGTAGAAGCTCTTCAAAGTTACTCGTGTCACCAGGCTGCCTTCCTGCCTCAAGAAACTATTTGAAAAAAAATCAAGGAATCATCTAGTAATAGTGAATTCTGTTTTCAGAAGTTTAGGGATTAGAAATTACCTGTCATGAAAACCCCATGGCTATTCGTTACAAGATTCCAGAGGAAAAAGAAAAGCTATTTCAAGAGTCCCACAATATGGGGCCACGGGTGTCATTCCCAAGCACCATCAAGAAAGAGTTTTATCAGTAAATACATATGTTGTAGCGTAAATTCCTAGAGCAACAAACCGACTTTTAATTCATGATGGCAAGGAAAGTACCTGTTGCAGCATTGAGTTACAAAACTGAGCATGGACTTCTCTAGCTTCGAAAGACCTAATATGTTGAATTACATCCTAG
Seq C2 exon
AGGCAAGCATTGATGACTTTATCCAGTCTGTGGAGCGCCAGAACATAGCTTTGGAAGTCGATGCTTCCGGAGCCAGAGATGGCACGGATGACCCATCCTTCAACGGAGCCCTTACAGTGTCTGGCGGTGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004040:ENSRNOT00000005489:19
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=0.044
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTTGGTTCTGGGAGTTGCC
R:
TCTCACCGCCAGACACTGTAA
Band lengths:
298-2047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]