HsaINT0153499 @ hg19
Intron Retention
Gene
ENSG00000050438 | SLC4A8
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 8 [Source:HGNC Symbol;Acc:11034]
Coordinates
chr12:51899619-51902980:+
Coord C1 exon
chr12:51899619-51899714
Coord A exon
chr12:51899715-51901209
Coord C2 exon
chr12:51901210-51902980
Length
1495 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
ATTGTAACACTTTTATTCAGTCT
3' ss Score
2.6
Exon sequences
Seq C1 exon
ATGTGACCCCTCTGAGATTAATATATCTGATGAAATGCCTAAAACTACAGTTTGGAAAGCTCTCAGTATGAATTCTGGAAATGCAAAGGAAAAGAG
Seq A exon
GTAAAGAGAACTGTAACATCTGGTTTTTATTTATTTCTGGCTTTTGACAATGGCGATATTGAAGGTAAAATGTGTTTTAGTTGTAAAATGGAATTTGTGTAATAAATAGCACTTCCAGGAACTGCCGCTAACCACATAAGAATAGCTATAAGCCTTAAAAAAGTAAAAATGTTTTCTAAATATTTGGTCAGGGTGTTTTAAGCAGCCCGTTTACACAGGTCCAAGGTCAGGAAGGGATTATTTTGGCATATAAATTTGCTTTGCCTGTTTATTTCCTTTAATCCTCTTTCTAGTTCTCATTTCAGAATCTGAAGGGCATGTCTCTGGTTACTGCAACCACACAAAGTAGGAAATTGCTAAAATATTCAGATAGTGTTGATAGTACTGATACATTCTTTAACCTATTTCACTTGTTACATAATGAGAACTAACAACAAGTAAAGATTTTTGAAATATTAAATTGTAACTGGTTTTTTTTTTCTTTCTTTCTTTTTCTTTTCCTTTTTTTCTTTTTTTGTTTTTTTGAGACGGTCAGTCTCTGTCTCCCAGGCTGGAGTGCAATGGCACAATCTCAGCTCACTGTAATCTCTGCCATCCGGGCTCAAGCAATCCTTCTGCCTCAGCCTTCCAAGTAGCTGGGAGTACAGGTGCATGCCACCCCTGCCAGATAACTTTTGCATTTTTATAGAGATGAGGATTTACTGTGTTGCCCAGGCTGGTCTGGAACTCCTGGACTCAAGGGATCCTCCTACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGGGCCACTGCACCCGGCCGTAACTGTTTTTCTGTTTTGAAACCAAATACCGTATATCATTTACTAATAGCATAGATCAACCTTAATCAGGTTAATGAAGAAAATGGAAGAACTTGAGGCATTTTTGCCTGCATTGAGGTAGGCTATATGCCAAAATTTCTTGAATAATTTAGTCCAAATACCATTTAAATATAAGTAAATAACTGAAGACAAAATCTGAGGCCTTCCTAAAGTCAACTTTTCTAGTTAAAAAAAAAAAGCTAGGAATTAGGAGACCTAGTCCTTCGATTAATTCCTTGTATAACTTGGCAGACCACTGTTTCTGGTGTTCAGTTTACTCAGCAGGAAAATGGAGATAATAATAACTAACTGCCCCACTCCTGAGGCTGCTCCAAGGAGAAACTGAAGTGCTCTGAAAAGTCACAGCCACCAGTGGGTGGTAGTGGTGATTTATGTCTTCATCGAATGGGTTAAAATGAATCTCTGCTGAATGTGAGTGAAATATAGAATCTTGTTTCCTTCGGAGGAAAATCCAGGCAGCTGTCGAAATGTATAACGCACATGGTTATTTTTAGTTGAGAACTAGTCTACTTGTAAATGAACTTAAAATATAGCCAGATCCAAATTGTGGTGACATCTTCAAAGTATTGTGTTAAAAGGAGGAATGAATCATATGTTCCCTTTTTGTCTAATTGTAACACTTTTATTCAG
Seq C2 exon
TCTCTTCAACTAAGAGTCTTTGCTGGGATGGAAGATTTGGGCCGTGTGGTGCCTCAGGGAAGTTCTGGTTACAGAGAAAATGGCGAGTCTCTCAGAGAAGAAGCAAGACCAAGTCTGGCCCTGTCCTTGGTCATCTCAAAGCCATGCCGAAGCATTCAGTTATTCTTGGTGTGCATTGGAAGGCATCCAGCTATCCCCATACCAGCAGCCAGTCACCAGATGTGAATGTGGAAGCAGAAGACCACCTCCTGTTGGTTCTTCTCCTCTTCCTTCTTTTTCTCTTTAGAACGGCCACCATTGAAGACCTAGCTTCCCATTTTCCAGACGTTTTCTCTGAAATTCTCTGCTGGCCTGCCAAGCCATATGGATTCATTCTGCCACTGAGGAGTCCTTCAGTGAGGTCCCTCTTCCTAAAGGACAGAGTGGGGAGTAGGAGGGGAACAGAGAGGACATCCTCTCTGGCTCTCCAGTGCTCTTAGTGTCTACAGGCTCCTAGGCAGCCCTGGGCCTTGGTTTGATTACCTCCCCTGGGGGATGCTGGTCAGACCCAGAGGTTGTCAGGAGGTCAGCTACCAGGAAGATCCATGATCTGGGCATTGGCAGTGCCTGCCACCACAGCCAGGAAGATGCCTCTGACCTGGGTGCATCTCCATCACTCCTTAGCAGCAGCCTGCATAACTGGCAAGAATCTTGGATGATACAAGAGCCAAGAAGGGACATTTGAGTTGTGTCGCTTAGATAGGAAAGGGATCCAGGGAAAATCAACAGTAAGTGAGGATGAGCAGTGTCTCTTGGTTTTCATTGAGGATAGAGTAAGAGATTGAGTTTAGATTGCAACAGAAGGAATTAGTTTAGATACCAGGAAGAACTTCCTAGCCTGAAGATTTGTCATAGTGTCTGCTTTCTAGATATCTGGGAAAGATTTGATAATAGTTGTTTGTGAATAGAAAGGAGGATATGATGTTTTTATTGGCCATTTTGCGGGACTCTTCGACTTCTTGCTGCTGTCTCTTGAGGATACATTCCAATTCCATCCTGGCGAGATCCAAGTGCTTACGTACTGTCTCCTTAGCTGCCTTAGAGTAAACGATCATCAGTTCAATGGACCAAAATCACCTTCAGCCATGTGGTTTCTTCATCATCATGGATTTCTTTTGGTTGACAAACATTCTGGCTCTCAGATGCAAAAAGTCACACTGGGAAATGAACTGTAAGTGGTGAAATTAGTTTTGGTATTTAATTTAAAACTACATTTATAGTTTTTCTCTTCTCTTCTATGTTGCAATGAATGTAAAGTATTTGGGATCCAGTGCTTATAAACCTTTCCTTCCTTTGTGCACAGAATGTAACTAGCAAGCCCATTAGCACCCAGATAATTCTATCATGTTAGTTTCCCATCCTGGAAAATCTTTGTACAGTGGGAAGTTCCCCGATGTGTTTTTCTTTCTTAGGTGAAGGGTTGGCTATATCACTTTATTGAATTTTGCATTCCTTAGACTTTTAAAATATACTAATGTATTCTAGTCTTACTCTAAAGACCTTTGATGTTAAAGGAATCCTTCATTTATTTCATATTCCCTATCTCATAGGGCCACAATTATTTTAATACAGAGATGATTTTCAAAATATTTTAACAACTGGTACAGGACAGATGCCAGCCACTCAGAAGGGATGCCTGCTGTAAACAAGCAGTATGTATGGTTGTACCAATGCCTATTGGCTGAACATTATGCTACTTTCAGATATTAAAATGGTGTTCCTTTGAATCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050438-SLC4A8:NM_001039960:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.121 A=NA C2=0.750
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACAGTTTGGAAAGCTCTCAGT
R:
GTCTTCAATGGTGGCCGTTCT
Band lengths:
355-1850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)