MmuINT0007898 @ mm9
Intron Retention
Gene
ENSMUSG00000028125 | Abca4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:MGI Symbol;Acc:MGI:109424]
Coordinates
chr3:121859256-121860876:+
Coord C1 exon
chr3:121859256-121859403
Coord A exon
chr3:121859404-121860752
Coord C2 exon
chr3:121860753-121860876
Length
1349 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
GCCTCACTTCTCTTTCTCAGACG
3' ss Score
8.48
Exon sequences
Seq C1 exon
ATGGGCAGTCATTCCTATGATGTATCCAGCATCCTTCCTGTTTGAAGTCCCCAGCACAGCCTATGTGGCTTTGTCCTGTGCTAACCTGTTCATCGGCATCAACAGCAGCGCCATCACCTTCGTCCTGGAATTATTTGAGAATAACCGG
Seq A exon
GTGAGCAGAACCTTCTTGGCTTCTTGGTTTAGTTGGTGGGATGTTCAAGCTGATGTAGCAGTCTGCAGAGCCATGGAGAACAGGGTATGTAGATGCACATACCCGGGAGAGCCGGGCTGTCTCCACCACCCTCGCTGGGCAAGACTCCCTACTCTGGAGTCTTGATTTATATTCTGTGAGTGCAATGGCTTTGTAAGCCTCTTCTATAAGTTACATACATTCACTCATGATTCTAACTTTTTAGAATAAAGGTAGAAAGCATGCACATGCACACGCACACGCACACACACACACACGCACATACAATGACATAGTCAGGTGATTTCATATAAGGACCATACACTTAACAGATTGTGCCACGGGAGCTTCTGTTCAAGTGACTCAAAATGTAAAAGAAACAAGAAGACATAAGAATGAAAAAGCTCCCTACCCACTTTGGGTCACCCAACTTCCTTCTCAAGACTCCACCTTATTCCAGTTCATAATGTTTTCTGAAGACAGACAAACAAACATGTATTCTTCTCCAATTTTTTTCGTACATAAATGATAACATACTAGCACATACCGTCCTGATCCCAAAGAAATTCTGAGGACAGATTAGGGAACCCTGGTGCCGAATGACTTAGTTTTACAAGATATTAGGTCCACTTGCCTTGTCTACACCCTCTGCTTCTTTGTCCAGAAGGAAATGCCAGACAGAGGCCTTTAAAAAGAGGGGAGTCGGTGGCTACAGTGCTGTCTGTCTTTACTTTTGATGACTCTCTCTGAGTTCTGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGCCATGATATACTATGCTATGGCTATGGCTATGTTATGACTATGGCTCTGCTCTGCTCTGCTCTGCTATGGCTATGGCTATGGCTATGCTATGATTATGGCTATGGCTATGGCTATGCTATGCCTATGGCTATTCTATGGCTATGCTATGGCTATGGCTATGGCTATGCTATGACTATGCTTATGGCTATGACTATGCTTATGGCTATGACTATGCTATGCTATGCTATGCTATGCTATGATTATGACTATGACTGTACTCCCAGCACTCCAGCTTCCTGGGGGTCTGTGTCACTAGCCTTTCCTTTTCTTACTAGTTCTTCACAGTTCAGAGGGTGGCCACACATCTGCACTGGGCCTCCCCAGAAGACCAGAGTGCCTGCTCTTGCTGCTGAAGCCATCAGAGCCTACTTGCTGATGAGGAGACAGGTGCCCTCAGCCTCCACGCTCCTAACAGCCTCACTTCTCTTTCTCAG
Seq C2 exon
ACGCTGCTCAGGTTCAATGCCATGTTGAGGAAGTTGCTCATTGTCTTCCCCCACTTCTGCCTGGGCAGGGGCCTCATTGACCTGGCACTGAGCCAAGCTGTGACAGACGTCTATGCCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028125-Abca4:NM_007378:38
Average complexity
IR-S
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(16.3=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(13.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGCAGTCATTCCTATGATGT
R:
CAAACTGGGCATAGACGTCTGT
Band lengths:
271-1620
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: