RnoINT0010229 @ rn6
Intron Retention
Gene
ENSRNOG00000012892 | Abca4
Description
ATP binding cassette subfamily A member 4 [Source:RGD Symbol;Acc:1309445]
Coordinates
chr2:225708098-225710170:+
Coord C1 exon
chr2:225708098-225708274
Coord A exon
chr2:225708275-225709947
Coord C2 exon
chr2:225709948-225710170
Length
1673 bp
Sequences
Splice sites
5' ss Seq
CTCGTGAGT
5' ss Score
8.41
3' ss Seq
CTTTCTTCCTCTCCCTTTAGCTT
3' ss Score
12.08
Exon sequences
Seq C1 exon
GTACTGGGATTCTGGTCCCAGGGCAGATCCTGTCGAAGATTTCCGGTACATCTGGGGAGGCTTTGCCTATCTACAGGACATGGTTGAGCAAGGAATCGTGAGGAGTCAGACCCCGGCAGAGCCTCCAATTGGAGTCTATCTCCAGCAGATGCCTTACCCCTGCTTTGTGGATGACTC
Seq A exon
GTGAGTCCCAGGCCTCTATCCTCCTCCCTGCTGAGAAGCAATAGATGGGGATGCTCTCGGGCTTCTGTGTCTCCTGAAAGAACCCCAGGGACAAGGACCAGATTGGGGAGAATAAGGTTCTGACTGAAGAAGATGTTGGTTCCATACTCCAGACAGAAGCAGAGGGGAAAATAAAATGATAGGGTGCTGGGGGTACAAAAGGGAAATTGGAGGTTAAAACAATAGGAGTGAGGTTGAAGGGGGTGCCAGCTGTTTAAATTTCCATTTCGTAGTATGTTTGGTATGTGAAAGTGTTCTGGTCAGGGTGTTTTCCCACTGATTGCCAGATCAGCAGATTCAGACTGCGAGGCAAGTAGGTCTGGTACCTAGGAGCCTCAGAATAATGCAGCTCCTTCCCTAATTAACATTCCTATGATGTATGTTTGGTGAAAAGGTAGAGGAATGTGTTGGATGAGCTCTGGCCTCCTCCTCTGACCACCCCCATCCTAATGCCTCCCCTTCCTTTGGTCACTAGCATGCTAAGCAAACAGTCTGCTGTTTTGTTGAAAATAGATTTTGGAATGGTGGAGAAAGGGACAGATGGGGTGGGGGGAGGTTCCCAGAAGGCTTATTATCATGGTAGATGGGGTCAGAAACACTCCCTGACCTATAGTTGGCTTAGGAATTTAACTCCTGGGGTGTTGAGAACACAGGAAAGTCGCTGTAGCATGGGAGTGTGGGGTCCCGGAAGCAGAGACCACAAAACATGGAGAAAAGAGTCCAGTCACCAGCTGGAGATTGTAAAATGAAGCCCAGTGTGCACCTAGGGAAGCGGCTCCCAACACTGTGGCCCCATCAGGCCTCCAGCTCTGCAGAGGACTGAGAAGAGAACAGTGGCTGTTCAGAAGTTAGTTTTCCTTTGGATAAGAGGCAGAGATGGGACGTAGAGCCAGGGGCAAGAGCCCAGGTCCACTTTCAGGGTCAGAAGGGGAGGGGCTGGCAGGAAAACGTTAAGTGTGAATAGCCTGTGGGAATTGAGTCATTCAGTATGGGAGAGTCCTCTGGCGGCCAACCCCAGAAGCGCATGGTTTTCGGTTGTTTGGTTCCCTCCCTAGGGCCATTTTGAGTGAAACTATCCTCCCACATTGGCATTGGGCCCTTCCTTTGACAACACCCAACAGTTTCAATAGATAATAATCCCAAGGGCTTTCCCAGTGCATTATTCACAAGGAAACCTGTAAAGCTCACCCTAGTGTAAGTCCATCGCGGCACATCTGTCCTGCCTGCTGAGAACCTATCCCAGGACCCACTCCACTTAAGAACAGCTGTTGGAATCAATGGCTCTTGAATCATCGCCTTGTTCCGATCGCAACCTATACCGGCAGGTCTACAGTCTTTCCCACAAGCTTTTATGGAGGAGATCTATACTATATGACAGAGATCATATAGTCTTATTCCTATACTTTATTTATAGAGCATCCATCCAGGCTGTCCAGAAAGGCTCTGTCTTACCTTAAAGAAAGACATGGCCAATATGAAAAGTATTTAAGAGGTTCAACCTAGTGAAAGTCCAGTGATTTATTTTTCTGCTTTCCTTTCCTTTGGACTTCATCCTCAACTCTCCATTCAATAAATATTTACATAGTCTCTACCAGGTACAGCTGGCTCTGTCTGCTTTCTTCCTCTCCCTTTAG
Seq C2 exon
CTTCATGATCATCCTGAATCGCTGTTTCCCCATCTTCATGGTGCTGGCATGGATCTACTCTGTCTCCATGACTGTTAAGGGCATTGTCTTGGAAAAGGAGCTGAGGCTGAAGGAGACCTTGAAGAACCAAGGTGTCTCTAACGCTGTGATTTGGTGTACTTGGTTCCTGGACAGCTTCTCCATTATGTCAATGAGTATCTTCCTCCTGACGCTGTTCATCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012892:ENSRNOT00000017878:13
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(17.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACATCTGGGGAGGCTTTGC
R:
TGAACAGCGTCAGGAGGAAGA
Band lengths:
350-2023
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]