DreINT0023595 @ danRer10
Intron Retention
Gene
ENSDARG00000013500 | abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:ZFIN;Acc:ZDB-GENE-050517-1]
Coordinates
chr5:24634337-24636085:-
Coord C1 exon
chr5:24635989-24636085
Coord A exon
chr5:24634511-24635988
Coord C2 exon
chr5:24634337-24634510
Length
1478 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TCTGTGCTTTCTCTCTTTAGGTG
3' ss Score
14.01
Exon sequences
Seq C1 exon
GTCAGTGTGGATATCTTCAGAGGCTTCCCTGATGAAGAAAGCATTGTCAATTACACACTGAACCAGGCCTACCACGACAACGTCTCAGTCTTTGCAA
Seq A exon
GTGAGTTAATTATAATAGTTCTCAAGTCATCATGAAACATCTTCAGAAAATTTGTGTTATATTTCATTCACAATTTAAAAGAAAGTAATATGACTAAGAGGGGGCGACACGCTGGCTCAGTGGTTAGCACTGTCCCCTCACTGCAAGATAGTTTGAGTCCTGGCTGGGTCAGTTGGCATTTCTGTGTGGAGTTTGCATGTTTTCCCTGTGTACATGTGGGTTTCCTCCAGGTGCTTCAGTACAGTCCAAAGACATGCGTTATATGTGAATTGAATAAACTAAATTGGCCGTGATGTACACTACCAGTCAAAAGTTTGGGGTCAGTAGGATTTTTAATGTTTTAAAATAAGCTTCTCCTGCTCACCAAGGCTGCATTTATTTAATCAAAAATACAGTACAAATTGTCAAATTGTGAAATGTTATTGCACTATAAAATAACTGTTCAAATGTAGTTTATCATTAGTTTTAGATTCCAGGGATTTTAATGATGAAATTTCAGCTTTTACTCGAGTCTTCAGTCACAAAATCCTACAGAAATCACTCTAATATTAATTATTATTGTTATTATTATTATCATTATTATTATTATTATTAATGACCATAGCAATAAATGCAATAATGACTAGAGTAATAATTGTATTAATACAATAAATAAATATTTGATAAATGAGTATTTAACGATTTATCTTTTTGTTTTACATTTATTAAATGCTGCCTTGTGTGAATGAGTGTGTATGGATGTTTCCTTGTTCTGGGTTGCAGCTGGAAGGGCATCCGCTGTGTAAAACATAAGTTGGTGGTTCATTTCGCTGTTGTAACCCTTGAAAAATAAAAACCTATACAGCATATTTTAATTTTAATGTTAATCTCAGTTAATCTCAATCTCTACTAATTCATATTTTTAAAGGTTAACTTTAGTTTAATGAACTATGAACTAACATGAATATACACTAACACTCTTAAAATGTTTTTATTATGAAATAAAACAGCTGAGAAAAGGCTTTTTAATATTTATGTTTTAGATTGTAATTTTTCCTATCAAATTGTGCCTTTAAAGTTGTGTGACAAAATGTCTGAACAATGTATAATCAAAATCAGTAAAGAGGTTTTTATATTGTTTTAATGCTACAAGAAAACCATATTGTGGTTGTAAGAATATTTGTCAAAAATGCTTGCCATAATGCATGGATCCTTAAGGAATTTTTGTTGTCCGGCCCAAAACAACAACAAAAAAGTTTCACTATTTGGATTCAAGTTAGGAAAAAAAAGATTCAATCATACACTCTTTTTGGCCAGGCAGTGTTGATTCATATATATATTTTTTTTTTAGGTTAAAAAATGCCTTTTTGTTAACAAGCATTGTGAGACCCATCCATTTCCCATTAAAACTACATTTTCATGATTCATTTAGCCCTTAGTCATACCTTGTTAAACTTAGCCAGTAGCCATATCTTTTAATCTGTGCTTTCTCTCTTTAG
Seq C2 exon
GTGTGATTTTCCAGACCAATAAAGATGGATCCCTGCCACCCCATGTTATGTATAAAATTCGACAGAACTCGAGCTTTACCGAGAAAACCAATGAAATCCGACGTGCTTATTGGCGCCCAGGGCCAAACACAGGCGGCAAATTCTACTTCCTTTATGGCTTTGTGTGGATCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013500:ENSDART00000141554:11
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=0.017
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(7.3=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(13.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGTGTGGATATCTTCAGAGGCT
R:
CTTGGATCCACACAAAGCCAT
Band lengths:
270-1748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]