MmuINT0147188 @ mm9
Intron Retention
Gene
ENSMUSG00000060961 | Slc4a4
Description
solute carrier family 4 (anion exchanger), member 4 [Source:MGI Symbol;Acc:MGI:1927555]
Coordinates
chr5:89626674-89628841:+
Coord C1 exon
chr5:89626674-89626787
Coord A exon
chr5:89626788-89628679
Coord C2 exon
chr5:89628680-89628841
Length
1892 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTTTATTTCTTTGCTTTAAGCCA
3' ss Score
4.9
Exon sequences
Seq C1 exon
GCAAGAAAACTGATCAGTGATTTTGCCATTATCCTGTCCATTCTCATATTCTGTGTAATAGATGCCCTAGTCGGCGTGGACACTCCGAAGCTCATTGTACCAAGTGAGTTCAAG
Seq A exon
GTGAGCGAGTGTCTCTTTTGCTTGTTGTTCAAACTCTTTCTTTTCTTTTATTGTGGTTTATTCTGAACCTTCAGTCAGTTTTGTGTAATTACCCATTTTCCCCTCAAAGCAACCCCCTATTAGGCTCATTTACAGATAGTCTAATTTCTTCACTAAAATTGAACGCCACAGTGAGGATCAAATTTAAGATTCAGGTTTTATTGACGTTCATTTTCAAATAGCATATAGTATTAATGAACCCTGCCTTATCTCTCTTAGAATATTTCAGATACTCTTATAGACCTAATCGGCCTGATTCATGCAGTAGTTCTGAGAAAGTGCACACATAGCTAGTATTGTTTGTTTTATAATCTACTAATGTTCACAGAAAATAGGAAAACGGCCCATTACTTCTTAACTAGTGGGAGCAGGCAGTGAAATTTGAATTGAAGCTTTTAAGTTCTAACTTAGTGGTGTTTCCCTTTTACCAAATTACCTGCCAGGAACGCTTATAATATGAAGCTTAATTGTTCAAAGAGGACAAAAAGAACTATGTAACTTTCTGAACTTAATGTATATATAGGTGTAATTTATAAAACTTACATGTCATTCATTTGTAGTTATATATTTATGTAGTTTTTTAGTTATAAATCCTTAACCTATTTTCTAGAAAAATCCTTACTCTGTGTTCTCCACTATTGAGATAATAATGTCAAACACTATTATGCTGATTGCAGCGTTGTGAAGCTGAGAGGGGATATGCATGCACACATGTACACATGTGACATTAAAGAATGTGTCTGGCATAATATTATATTTATTAGCAAAGATAAATTCTGGTTTGATTCAATCACTAATCCATTTAAACCACTATTTTTTTTTCTAAACGTTTGAATGGAGGCAGTCCCCATCCGGTTGTGGTTGAAGGTTGAAATGCTTTAATGAGCAAGAGGAAGTGGTTTGCCTTACAAGCTCACAGTGTGTGATACAGGCCATGTGAGGATGGGTTTTGTTTCCATGGTGGAGTTTTGTGCAAACTGGATCATGCATCCAGGGTTTGTGGACTATGCCTACCAGCCCAGTACTCAGAAGGCTGAGGCAGGAGGATTTCTACAAGTTCAAGCCTAGTCTGGAGTTACATAGGGAATTTGAGGCCAGCCTAAGCTATAGAATAAGACTCTGTCTCCTAACACACACACACACACACACACACACACACACACACACACACGACCCAAAAATAAAAACCCCCAAAACAGAGGACCAAACTCATAAATAATATTATATTTACATCTACTTGCTTTTATTAAAGTTAGAATTAGCATAGAATGTTCTCTTCCTGTACCAAACATGTATGATCTCCAGACAGATGGAGATTAAGAACTTTTCTGGTTTTCTGACACAGTTCTGGTCATTTAATGACTTCTGGATAATTTTCCTATGTGAAGTAAGAGATCTGAGTACTTAGTTCAGGTATAACATGTACAGCTTTTTATGTGTTATGAAGCCATTTATTTTGCAGGAGTAGAAACTATTGTTAAATATTAAACTTCAAACAAAATCCATGGTGGCTTTGCAAATTTTTATTTGCTACCTCTTCTTAAAATATTACATTTGAGGCTTATTTCTGTGTCCCTTAATGTTAAATTTTCCTGTTTTTTCTCTTATACTTTAGCTCAAATAATTTTGTGTATTCAAAACATCACTCCCTGTTTTATTCAGTAACCCATGTTTTGCATCTTTTCTTTAGCAATTACTTCAAAAATAACATCTTTTGGGAAGGCTCTGTTAATTTTTTTTTTCTGGACTATAATTGTTTCTACTTTTAAAAAAGTAACACTCAAAAATTAAAAATTTAAAACCCTGTAGCATATATTACACTGTTCTGAAAAAGTTTATTTCTTTGCTTTAAG
Seq C2 exon
CCAACAAGTCCTAACAGGGGTTGGTTTGTCCCGCCATTTGGAGGAAACCCTTGGTGGGTGTGCCTTGCTGCTGCCATCCCGGCTTTGCTAGTCACCATCCTGATTTTCATGGACCAGCAGATCACCGCTGTGATTGTGAACAGGAAAGAGCATAAACTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060961-Slc4a4:NM_018760:17
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:
PF0095516=HCO3_cotransp=FE(7.1=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(10.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAAACTGATCAGTGATTTTGCCA
R:
TGAGTTTATGCTCTTTCCTGTTCACA
Band lengths:
271-2163
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: