MmuINT0147226 @ mm10
Intron Retention
Gene
ENSMUSG00000068323 | Slc4a5
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 5 [Source:MGI Symbol;Acc:MGI:2443220]
Coordinates
chr6:83265673-83267560:+
Coord C1 exon
chr6:83265673-83265760
Coord A exon
chr6:83265761-83267405
Coord C2 exon
chr6:83267406-83267560
Length
1645 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
CCTTCTCCATTCCTCACCAGCTA
3' ss Score
6.81
Exon sequences
Seq C1 exon
ATTTCTGTTCATACTATTAGGACCTTCCGGGAGAGCAAAGTCCTATAATGAGATTGGCCGAGCCATCGCAACCCTCATGGTGGATGAT
Seq A exon
GTAAGTAAAGATATGAAGCACACACTCCTTTGTGAGTGGTAATGGCTGTTGCACTGGCACAGCCTCCCCCACTCCCTGTCATCACCAATTATCTAACAAGCACCTCTGAGCCCCTGCTGTGCACCAGGGAACTCAGGATTATAAGATTCCGAGAATAGAACCAGACCCTCTCTAATTTAGAAGCACTATCCAGAAAGGGGGACAGATCTGCAATAATGAGATGATTAAAAAAAAAATAGAATTAACCATGTGCTGTCTGCCTGGGGAGCCAGGGCAGGCTCTGCAGATAGAAAACTAAGTGAACAGAAGGCAGGTAGACTGGCATGGCCCTGAGATGCTAGCCTTCTGGAAGCTAATGGAAGTTCAGTAGTGTAAGCTCAAAGTGTGCACTCCCCCAAGGGCCAGGGCAGTGACCTGAGCCAGAGGCCATACACACCCTGGGACAGGCAGGAGCCTAAGGGTCCTGTTCTGTCCCCAGATCATTGGGGAGCTGGAGGTCTTTAAGCACATGAATGACCCCACCAAATCTGCAAGTCTTTTTGTAGCCTGACCTGCTCCAGGGTAAAAGTATGGGCAGTAATGAATGGATTTGAAAACTGGACTCAAACTGGGCTCTGTAGAGGTTTTCTTGTGTGCTTGCTCTGTGGAAAACAGAAATGAAGAAGATGGGGGAACTCAGCAGACGTCCTACAGTAGTCTTAGCTGGGGTCGGCATCTAGGATGAGCGTGCCCAGGTTCCTTGGCCCTTGCTCAAAGACTTGGTATACAGCCACACAAAGATTTGCAGAAGCAGTAGGGGGACTTGATTCAAAGCAAAGAGACAGAACAGGTCAGGTACAGTCAAGAGTGACTGTGGGCCACATGAGTGAGGGTACCCAGAGACCCCAACTATTGTTTGGGGTTTGTTTTATGGGGTTCAGAGGAAGGTGGAGTGTTAGTATGGGTGGTTCTCTAAATGACAGACTAAATTATATGACCATCTTTCTGTTGTGAATGTCCCTTCCCATCACACATCTGATTTTGATCATATGTATACCTAATTTTGCATAGGTATAAGAAGTTTGATTTATTATAAAAACCTAGCTCAGGACGTCCCTAGTTTCTTATCCAGACACAAGGAGAGTATCATTGAGTAGAATTTATCTATGTTTGATGGTTGTTAAGGGGAGGAGACAGTTCCATTGTTCAGAGTGGAGTGTGTGTACAGCTCAGTGCAGGTGAGGGCCCTAGGTTGCTAATAAATTGCTAGGTATATGTGCAGAAAGGCATATGTGTACATAGTATAGTATAAAGGTTCTAGGCTGCTAAATGCACTATTAGAAGAGGTGAATGTAGGTAGCCCACATTAAGAGGAGTCCCAGGTTGGTAAGCTATTCCCTATGCTTGCTTGTCTCTAATGTATCTCGGAGGCATAGGTTTCTGATCTCAGATGACCGCCTGCTCTTGGAACTGGCTCTTTCCTATTGTTCCCTATTTCCCTTACTGTCCTTTGTCCTTATCCACCCACTGGAACCAAGTGGGCATCCTGAGAAATGGCTAGAATTGGTTCCTTTAAAGATAGCTGTGATGTGCTCACTCCCAGGAGGGGAGGACTGAGCCCTCTTTTCTCCTTTCTGCTTTTTTATCCTTCTCCATTCCTCACCAG
Seq C2 exon
CTATTCAGCGATGTGGCTTATAAAGCTCGGAACCGAGAAGATCTGATCGCAGGGATTGATGAATTTCTAGACGAGGTCATTGTCCTTCCCCCTGGAGAGTGGGACCCAAACATCAGAATTGAGCCACCCAAGAAAGTTCCCTCAGCTGACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068323:ENSMUST00000113899:8
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=0.192
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(10.8=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(13.4=69.2)
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:
TGTTCATACTATTAGGACCTTCCGG
R:
CTCTTGTCAGCTGAGGGAACTT
Band lengths:
238-1883
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types