HsaINT0153299 @ hg38
Intron Retention
Gene
ENSG00000004939 | SLC4A1
Description
solute carrier family 4 member 1 (Diego blood group) [Source:HGNC Symbol;Acc:HGNC:11027]
Coordinates
chr17:44255673-44257544:-
Coord C1 exon
chr17:44257350-44257544
Coord A exon
chr17:44255847-44257349
Coord C2 exon
chr17:44255673-44255846
Length
1503 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
3' ss Seq
GCCTTGGTTTTCTGCTGCAGATC
3' ss Score
10.74
Exon sequences
Seq C1 exon
TTCTGCGAGACCAACGGTCTAGAGTACATCGTGGGCCGCGTGTGGATCGGCTTCTGGCTCATCCTGCTGGTGGTGTTGGTGGTGGCCTTCGAGGGTAGCTTCCTGGTCCGCTTCATCTCCCGCTATACCCAGGAGATCTTCTCCTTCCTCATTTCCCTCATCTTCATCTATGAGACTTTCTCCAAGCTGATCAAG
Seq A exon
GTGGGGGCCTATGGGGATGTTAATGCACACGGGAGGTTGTGTATAAGACTGAGACAGTGGCCGGGTGCGAGGGCTCAGGCCTGTAATCTCAGAACTTTGGGAGGCCGAGGCAGGTGGATCACCCGAGATCAGGAGTTCAAGACCAGCCTGACCAACATTGTGAAACTCCATCTCTATTAAAAATACAAAAATCAGCCAGATGTGGTGGCATGCATCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACTGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATTGTGCCACTACACTCCAGCCTGGGCAACAGAGCAAGAATCCGTCTCAAAAAAAAAAAAAAAAGACTGAGCCATTGTGTCCTCGCACATGTGTCTGTGCAGCATTTGTGTGTCTTTGCTTTCACCTGTGTACATAACCATGTGACTGTGCACATGACTGTGACAACATATGTGTCTGTGTCAACATATGTGTCTATGTCTGTGTAGTCACACATCTGCACACAGGACTGTGCAGCTGTGTTGACTGTGACCACATATGTGTTGGCACCTGCTGCCTGTGGCCAGCACTCTTGCTGAGGCATGAGAGGGTGCCTCTGTGTGCACATGTCCAGTTCATGACCACACATGACGTGAGCAATGGGTAGGTATGGGCATGACACTGAGCATGTGAAAGTACATGCACAGTGAGAGCTGGGGGGACTCTGGAGCCTCTGAAGTCCCCCACTCCCTCCCCTGTGCTTGTCCTCAAGAGCTGCAGGGCTTGTGGATGGAGTGCCCAGCCACCTTGGCTTGGCTCCCATCATCTTAAGCTCTGCTTGCCTTTGTACCTGCATTTTATATGGGAGAAGGGTGAGCCCTATGTGTTGTCCCCTGATTCTGTTGGATGGAGGGTCTTTCTGTGTCCAGGTCTTTTAACCCCTTGTTAGAAACTTCCCTGACCCTTGTTTCCTGACCTCCAGCCTTCTCATGTCTCCCAGGTCCTGGGTGTACATGTGTGCTCGCACACACACCCATTGCCTTCCATGGCCCTCCCTGCCTAAACCTAGGCTGTCTTCATTCCTGAAAACCAAGCTGTAGAATCCCATTTATCCTCTGTTTCCATGTCAATTGAGGAAGAAGATAGATGGATGGATGGATGAATAGATGGATAATGGATGGACGGATGGATGGATGGATGGATGGTTGGATGGATGGATGATTGATGAATGAGTGGGTGGATGATGGACGGATGAATGGATGGATAAATGGGTTGATAGATGATAGGTAGGTGGATGGATGGGTAGATGGATAATGAATGGATGGATGAATAATCAATGGATGATCAATGGATAATGGATAGATGAATGATGGATGGGTGGATAAATGGATGGATGATGAATTAATAGATGACTGGATGAATGGATAGTAGTGCTGGGTAGAGTTAGCTGGTGGTATTTTCCAGCCCAAGCCAAAGCTGGGAGAGAACAGAATGCCTTGGTTTTCTGCTGCAG
Seq C2 exon
ATCTTCCAGGACCACCCACTACAGAAGACTTATAACTACAACGTGTTGATGGTGCCCAAACCTCAGGGCCCCCTGCCCAACACAGCCCTCCTCTCCCTTGTGCTCATGGCCGGTACCTTCTTCTTTGCCATGATGCTGCGCAAGTTCAAGAACAGCTCCTATTTCCCTGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000004939:ENST00000262418:13
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=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=FE(32.7=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=PD(11.7=39.7),PF0095516=HCO3_cotransp=PU(15.5=75.9)
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:
TCTAGAGTACATCGTGGGCCG
R:
TGCCAGGGAAATAGGAGCTGT
Band lengths:
350-1853
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains