MmuINT0007550 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53043661-53048452:-
Coord C1 exon
chr4:53048209-53048452
Coord A exon
chr4:53046956-53048208
Coord C2 exon
chr4:53043661-53046955
Length
1253 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
GTCTGTCTTCCTTTTGCCAGGTA
3' ss Score
10.17
Exon sequences
Seq C1 exon
GTTTGGAGATGGTTATACAATAGTTGTACGAATAGCAGGCTCCAACCCTGACCTGAAGCCTGTCCAGGAGTTCTTTGGACTTGCGTTTCCGGGAAGTGTCCTAAAAGAGAAACATCGAAACATGCTTCAGTACCAGCTTCCATCCTCCTTGTCATCTCTAGCCAGGATATTCAGCATCCTCTCCCAGAGCAAAAAGCGACTCCACATAGAAGACTACTCTGTCTCTCAGACAACACTTGACCAA
Seq A exon
GTAAGCTTTCAGTGAAAAGTACATTTAGCTACAGGCTTGGGATGCCTGCTCCTTTCTCCCCACCATCAGCTTGAGAGAACTTCAGCCTGTGCTTTGATTCCATTCCTGCTATTACTGCCTATATTATACAGATTTCTGTGGGCACATGCAAAACGTTGATGCTTTCTACTATATATAAATTGTGACTGTAGTAACAGTAGTCACAATAACTACCATTGATTACCTGTCATGAGTCAGGCATTTTGCCAGAAGCATTCTCTCTTCTTTTTTTCCTTTTTTCTTATCATTTTTTATTAGATATTTTCTTCATTTACATTTCAAATGCTATCCCGAAAGACTTTATCTCTTCTACATAACAAGATATCCTGTAGCAGTAATCTGTGAAACTGCTCTGAGGTCCTAGCTGATGATCACATTTCTCGCCACCCACGAGAGTTCTCTGGATCCTCGAAATAAAAGACACAAACACCCGAGTTAATTTTAATATGCCCTCACTGCACAAGGCTGGGCTTCTCCCTGACTTCATGTGGCTAACCCACTCTCCCCTCTGATATTCCAGAGTTATCACCTTTTAAAATCTATATTTTATCTCTACTGCCCCAGACACACCTGGGGGATTGGCCTGGGGATGCTTTCCTGACTGCCCCATGGCTGGATAATTTCTGTCCTGCAGCTCTTAGATCTGACCTCTCTGCTTCCCCATCACGGTCATGGTGATTCTGACCCTCCTCCTTCCCTTAGTCCTTTGTCCAGGAAATCTAAAATTCCCACCTCCATCTCCCTGCCCAGCCATTGGCTGTTAGTAACTTTATTGGCCAATTAAAAACTAACTGGGGACAGGGACCTTCAGCAATTGGACGTGTATATTCCTGTGTGATTGTGGGAGCCAAATTAAGACAATGCATGAGAACCAATCCCCAGCAATATACCAGACAGAGCTTGGCAGTTAGTAGGTATCCAGCAAGTATTTTTTCATTTCCTCTTAATTAATCCTAGATATGCTAAAGTGGATGATTGATAAATGGGTGGTTTAAATAGTTAGTGATGTGGGTGATGTAGAAAAGGATTTCAATGCATTCTGTGCTTCTCGAGAGCTCTCCCTTTCATGGGGGATTTCTCCTTCAAGTACTTACTCAATTCTGTGTTCTCCTAATCTCAACACAAGGAAAAATGCCACCATAAATAAAATGCAGCTACAACAACAAAAGATTCAGTGCAGAGGCCTTCATGACCGTCTGTCTTCCTTTTGCCAG
Seq C2 exon
GTATTTGTGAACTTTGCCAAGGACCAAAGTGATGATGACCACTTAAAGGACCTGTCACTGCACAAAAACCAGACAGTTGTGGATGTGGCCGTTCTCACATCCTTTTTGCAGGATGAGAAAGTGAAAGAAAGTTATGTATGAAGAATCCCGTTCACACAGGGTGAATGAAAGGAAGGAAGAGCGAGGTCTTCCTTTGCACTGTGTCAAGTGTTCTAGAAGAAAGCGTCCTGCGTTTCTGTGGAGAAGAACAAACTGGATACTGTACTGACACTATTCAATGCAATGCACTTCAATGCAACGAGAACACAATTCCATTACAGGGGCAGTGCCTTTGTAGCCTATGTCTTGTATGGCTCTCTAGTGAAAATGACTTGAAGTTAGTTCATTACCTTATACAGATGTGAAACTCTGGTGTGGAACCAAGCAGACTCTGGGTTTGGATTCATACTTTTTTTGTTCCTGTGTATTCTCACTAGGATTGCAACAACAGTCTATCAAATAGTCATGGCCAGTGATAATCAAAGTCAAAGGCACACACATCCTCGTCCATTAAGCCATTAAGCCATGCTGAACCACAAAACAGGTTTCCCGGTGACACATCCATTGCTGGCAATGAGTGTGCCAGAGTTACTAGTGCCAAGTTGCTCAGAAAGTCTGAAGCACTGAGTGTGTCACAAACACTTTTGTGAAAACCGCCCTACTGTCGGTTGACATCATTAAATATCAGGTGACAAAAACGGTGCCACATGTGACTAAATCCCCATTTTCCTTCTCTCTTTGATGAGCTGCTGTTGTGGCTGTCTTGTACAAAATGTGCATCTCTCTAACCCAGGTACTTGGTTCTCTTGTTCAGTGTTGCCCATGCCCCTGTCATGGCTTGCCATAGCATCTTTCTGAGACTTTTTCAAATACATTAGATCCTCCTAAGCAGCAAAGATTAGCAGCCAAACTGCTGGGGCTGCAAGCGGCTCAGTTCAGGGTGTGGCATGAAAGATCCAGTGCATTTACACGTGGCAGGTCTGGGTTGGTTTGTGCTGACTGTCTCCTAACACAAGATGGGTACACTACACCTTGAGATCCTTCATTATTTAACAGAAATCTAGTTCTTTCTAACTGTTTGAATTAACCTAGAAAATGAAAGGGTGGCATTTCATTTTGACAAAAATGTTTGCATTGTTAGTATTATTTGGAATTTTAAGTTTTATCAATGCTTCTGGAAGCTTAGAACTGTACACGTGTGATGTCAGTCACATAGAGGAATGTGCCCGGACTGCCTCATGCCTTTATTTTCCTTGGTAAATTTGAAGATAGAATGTCTGACTAGCGCAGTGACCAGAAAACAATGTGGTAGTCAACATCTCAGGCCATATTTTAAGATCCTGTAGAGCACTATTCATTTCAGGTTGCAGATGGAGTATTTTTGAAACATCATTACTATGTAGATGCTTGGATAGGAGTGAGGGGGAGCTAGCAGATTTCCTGTGCCATTTATTCAGCTGATTGATGTACAGATGTAGGTTTATTTTGTAAAATCCACTGAAAGAATATGGCCACACCCTTGCCTACTTGATAGCATCAATACAGAAGCCAAGAAGGACCACTAAGTAACCCCCTCTTCCCAGGGAGAGCAGCTAGCTTGAAATCTCTCGGATACAATCGATGCGTCTGACCTTTGGGATCCTCACCATATGGGCAAACAATGGGCTTTGCAGGATGAGAGACACCCACTTAAACCTCTGACGATCTCGAATGGTTCATCTCTTCCGTCATTAACCAGTCATGGAAAACAATCAACAAACTCTGCCACGTGAAATATTTTTTCAGACTTTTCTAACCCAAGCTTAATTTGTTTTCATCTGCAAGCAACGTGGAAAAAAATAGTTATTTCACCAGTGCTCAATGTCATCCGTCTTCATACAAAACAAAAATATGAGTAAGTTCCTGTATTGGGCAAAGTTCAAGTGAGCTTTTGCTATCCTTATTTAACTTCTTCTAAAAATTTGGAAGAATAAGATTTCAGATCTATTTCAAATTATGTTTATATAATGTTATGTAATTCATTGCTTGAAAGGAAAAATGACAAGTTTGATACTAATGTCAACATAGGTTTCTAAAATGATAAGGAAAGTGTGTTTCCAGTAGTTATTGGCATACCATTCATTTTAGATATCAAAGATACCGAAATCAAAGAAGCATGTCTTTATTTTTCAAAAACAAACTTCCGTTGGCTTTCTCAGTCCATTATCACCATGTACAGCCCTTAGAAAAATCCTTGTTTTAATTACTCAGATTTTTGAGGCCACAAAACAACAACAAAAGTAAGGCACCATTTTTGAAAACAAAATCAATTGAGTGTAGATTTAAAATCTTTTCTGAAGCTAGAGACAATCTGTAGCTATTATGTTACCTTTTACACTATCTGAAGAGCAATCTTCAACTTTCCTGTTTAAACGTAATTATTTTAGAAAGTTAAAAATCAATCCTATCTTCAAATAAGAATTTCTTAGATTCCCTATGGAGATGTGCATTGTGAGTTGAGAAATTCTCAAGTGCAAACACTTCTGGTTTACTTTAAAAAAAAATAGTGGAAAACTTACTAACTGTGAATATGAGAAAGACAAAAGAAAGTGAGTCCTCTCGCTAGATATACCTAGCATAATTCATTATGAAACAAACAAACCTCAAACTACTGTATTTTGGTGTCTGTACCGCAAGCATATGCCTCATGACTATAAATGTTACATACATCATTTGCTCTCTGTATAGTAGGCATTGACTTAAAGGGATTGTTTGTTGTCTTCTCATGGTTGTATATATCAGGTAAAATTGTTCCAAAGAGCCATGTGTTATGTAATGGGGAACCACTTTGATACTGAATTACTAATTTGTACTTTCATTACTATTTGCTGGTAATAGTGTAACGCCACAGTAATACTGTTCTGATTCAAAACTGTTGCATCCCTTTTTGTAGAACATTTATATTTCCATAAGGATTCGGTATGTTCTTTTCCCTCCTGCCCTAGGATGAAGCTGGTTTTGTGCTTTTTCTTTATCATTGGCCCTCATTCCAAGCACTTTATGCTGTCTGTAATGGATCTATTTTTGCACTGGAATATCTGAGATTTGCAAAACTAGACAAAAGTTTCAGAGCAGATTTCTAAGTTAAATCGTTTTCATTAAAAGAAAAAAAAACTGAAAAAAATTGTATTGTGAATAACTTTATATGACGTGTTTTTTTAAAAGCTTGTTTCTATGTTATGAGTCACAAAATAAAGCTGTGACAGTCCTGCTGGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:49
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAGCTTCCATCCTCCTTGT
R:
TTCTCCACAGAAACGCAGGAC
Band lengths:
358-1611
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: