MmuINT0147063 @ mm9
Intron Retention
Gene
ENSMUSG00000006574 | Slc4a1
Description
solute carrier family 4 (anion exchanger), member 1 [Source:MGI Symbol;Acc:MGI:109393]
Coordinates
chr11:102215580-102217585:-
Coord C1 exon
chr11:102217391-102217585
Coord A exon
chr11:102215751-102217390
Coord C2 exon
chr11:102215580-102215750
Length
1640 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CAAAGTTTTGTCGGTTACAGATT
3' ss Score
6.75
Exon sequences
Seq C1 exon
TTCTGTGAAAGCAATAACCTGGAGTATATCGTGGGCCGCGCGTGGATCGGCTTCTGGCTCATCCTGCTCGTGATGTTGGTGGTGGCCTTTGAAGGCAGCTTCCTCGTCCAATACATCTCCCGATACACCCAGGAGATCTTCTCCTTCCTCATCTCCCTCATCTTCATCTATGAGACTTTCTCCAAGCTGATCAAG
Seq A exon
GTGAGGCCAGGGAGGATGCCAACACTCAGGCATAGCGTGTCTGTGAGAGTGTGTTATTATGTAAAAAGTCTGTACGGCGTGACTATGGCCATGTTTCTGCCTCTTTGCACAACCATGAACATGGGCACATGTATGTTTTGGGGTTCACCTAGGATTATGCAGCTGGGTTTCTTGGGGCCACGTAAAGGCTTGAGACTCAGTGCTCATGGCCTGACTGTATATGAGGGAAGGTACCTCTCTCAATACTTGTTCATGGTTATGGCCACACATCATGTGACTAGTGGGTACTATATGTGAGATGGCCCGGGAAGTCCTGTGCATCGAGGAAGTGGATGCTTTGAAAGCCCTAGGCCTCTCCTTTCCTGCACTTGCCCTCCAGAACCCCACAGGGCCTCTGCCTCCAGAACTTGCCTCCTCCCCATAGAGCTCCACCCACCTCCACATCTGCACTGTGTATGGAAGAAGGGTGACCTGTGTGTGCCTGTCCTTATTCTGTTGATTGGCAGGCTCATTTATGTTCTGTAGATCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCAAGACAGGATTTCTCTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCTTGAGCCACCATGCCTGGCTCTCTGTAGATCTTTTAAGAAGATTTTTTTTTTATTTACTTATTTACTGTGCTGCGGTCCAAACCTCTTGCATGCTAGGCAAATGCTATCCCTGTCACTAACTCCTCAAGCCCTTTTTATTAACCTTCTTATTACTTAATGGCTATCTCCAGAATTCTCATGTTCCCCACAACGCCTGGAAGCATATACCTGCACATGCAGTCTTGTTGCTTCTTGGACCCTTCCCAGACAAGCTAATTGTTCTTCCTCCCTTAAAAAATAAAGCAAGGTGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTCCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACTACATGGTGGCTCACAACCATCTGTAACAGGATCAGATGTCTTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTCAAATAAATAAAAATAAATACACCTTAAAAAATAAAACAAGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAAAAACAAACAAACAAAAAAACAAACAAACAAAAAAAACCCCAAAAACAAAACCCAAGTAGGTTAATAAATCAGATGAGGAAGAAGAGACAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGTGTGAATGGGGAGATGGGTGTAGGTAGGTGATGGTTGTATGGGCAGTAGATGTGTAGATGGATGTTTGGATGTATATATGGATAAATGGATGAACAAACAACTGATTGATAGTGCCCAGTCAACTTATTTGATACTGTCTAGCTCAAGTCAAGGCTTGGATGGGGAACACAAAGTTTTGTCGGTTACAG
Seq C2 exon
ATTTTCCAGGACTACCCACTACAACAGACTTATGCCCCTGTTGTGATGAAGCCCAAACCTCAGGGCCCTGTGCCCAACACAGCCCTCTTCTCTCTTGTGCTCATGGCTGGCACCTTCCTACTTGCCATGACGCTACGAAAGTTCAAGAACAGCACCTACTTCCCTGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006574-Slc4a1:NM_011403:13
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(33.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=PD(9.9=33.3),PF0095516=HCO3_cotransp=PU(16.1=80.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTGGAGTATATCGTGGGCC
R:
CCAGGGAAGTAGGTGCTGTTC
Band lengths:
346-1986
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: